Adaptation-Induced Plothole

So you're watching the movie version of your favorite book, and wait- wasn't Alice's sword broken two scenes ago? What happened to the scene where she went to go get it reforged? And why is Bob seemingly flirting with Charlotte? Doesn't he indicate in the third book that he never liked her and suspected her of being a traitor?

Almost no adaptation is perfectly accurate. Details often get left out of adaptations, and sometimes this works, sometimes this doesn't (particularly to those unfamiliar with the original work). Other times, details are added that seem perfectly fine at the time, but end up directly contradicting canonical plot points - with a continuing work, this may even be a plot point the original writers hadn't actually written yet. Sadly, authors are not psychic.

If added material results in a plot hole, it may require an additional scene to Hand Wave it away. If removed material caused the problem, there may be a brief Info Dump to fill everyone in on what they missed. Contrast with its inverse, the Plot Tumor.

If this is caused by a work being translated into another language, it's a Dub Induced Plot Hole.

If there is simply a lack of explanation as to why something happened, instead of a full-on Plot Hole, it's Adaptation Explanation Extrication.

Anime & Manga

 * In a One Piece mini-arc about Coby and Helmeppo, the two are shown sailing over Reverse Mountain with Garp. Later on, it is revealed that Marine ships can cross the Calm Belt with special Seastone equipment, and the newspaper photo is hand waved away as a deception for the press.
 * The Warship Island Filler Arc makes two: first when Zoro easily cuts through steel chains, despite it being a plot-point in the canon Alabasta arc that he couldn't cut steel. Second is that all the Strawhats meet Ryuji, a dragon, which makes Zoro's comment to Ryuma in the Thriller Bark arc that he doesn't believe in dragons seem completely retarded.
 * Later in the manga, the crew meets a dragon for the first time, with all of them expressing surprise as they have never seen one before. Whoops.
 * Another one was when a Filler episode had Chopper use two Rumble Balls a short time apart without consequence, when it was later shown taking more than one within six hours has dangerous consequences; taking two should have made him lose control of his transformation.
 * Several in Naruto:
 * Naruto claims to have only read 10 pages of Jiraiya's latest novel, Make Out Tactics, in the anime as an extra joke that he was lying when he distracted Kakashi by pretending to spoil the ending. However, later on, it's revealed that Jiraiya asked him to proofread his books, and he at least obliged to the degree he.
 * A Filler episode expanded Suigetsu and Sasuke's trip to get Zabuza's sword from the Land of Wave, and it's mentioned that Inari and Tazuna would be working on a job in the Cloud Village for the next year. However, in the manga they actually ended up making guest reappearances in a job in the Leaf Village what was at most a couple months later.
 * A smaller one is how the anime gives the Fireball Jutsu to various characters that aren't members of the Uchiha clan or officially unable to perform Fire techniques.
 * During Itachi's fight against Naruto and Kakashi in Shippuden, it is stated that Itachi's Sharingan is not affected by the Hidden Mist technique. This contradicts what happened in the Land of Waves arc, where Kakashi's Sharingan was rendered useless against Zabuza's technique.
 * Omake should probably not be considered canon in general, but an early Shippuden omake has a really noticeable one where Deidara casually asks Kisame what Itachi is like as if he's never met him, even though Deidara was (forcibly) recruited into Akatsuki by Itachi in the first place and Deidara had spent the last several years trying to find a way to kill Itachi.
 * One Filler episode had Hinata learn a unique, powerful technique featuring a myriad pinpoint-precision chakra laser beams. Later in the manga, a major villain is able to curb stomp her using his powerful gravity blast attack- she spends the fight repeatedly charging at him while trying to land a physical hit, which is hopeless. The chakra lasers would have obviously been a much better bet.
 * In the anime Madara is able to suck Fu into his Pocket Dimension without touching him, while in the manga it was not clear if he touched him or not and it was later explicitly stated to require physical contact, which was exactly why
 * Death Note's anime adaptation omitted several scenes from the manga, which while usually not problematic, have led to plotholes. In the manga, it's explained that  This is not explained in the anime, but in the Relight 2 special,
 * However, while fixing one plothole, said special creates another: as  is ommitted in the process, leaving plotholes regarding   as well as how Light was
 * Also in Relight they have one scene where Light says to Ryuk that talking with him would be impossible
 * Bleach has a seemingly minor scene in the manga that was cut from the anime in which Isshin calls out to Kon in Ichigo's body, without using his name. and it is shown that Isshin is aware of who Kon is, he reveals that he never called Kon "Ichigo" while he was in his body.
 * In an early episode, Sora tears off his hollow mask and temporarily regains his sanity, but in the manga we don't see if he tore it off or it just came off by itself while being purified. It's later revealed that hollows, by tearing off their masks, become Arrancar and gain Shinigami powers, implying that unlike as shown in the anime it came off on its own.
 * During Episodes 8 and 9, a Shinigami comes to the world of the living in search of Rukia. In the process, he and Ichigo get into a short fight, and it later contradicts Ichigo's later claim that while his sealed zanpakuto looks large compared to Rukia's, he couldn't compare it to anyone else's.
 * In the Yu Yu Hakusho manga, the group uses Yanagisawa's Copy power to copy Kaito and use his video game skills to win a round against the Game Master. In the anime, the group uses Yusuke (who is otherwise not very good at video games) to win a fighting game, which makes their desperation to win when Kurama comes up seem strange; in the manga, only Yusuke and the non-gamer Hiei were left, but in the anime, they could have utilized Yanagisawa's power.
 * In the Fist of the North Star TV series, during an episode where Jagi terrorizes a village while pretending to be Kenshiro, one of the villagers remarks that Kenshiro was the one who defeated "Devil's Rebirth and the Fang Clan". However, not many people outside Jackal and his gang were even aware of Devil's existence. In the original manga, the villager simply said that Kenshiro defeated Jackal instead. This change was likely done due to the fact that Jackal was an independent villain in the manga, whereas in the TV series he was simply a lackey of Shin.
 * Code Geass gets a couple in the manga adaptation of the series, mostly brought on by the fact that it lacks Humongous Mecha but attempts to tell the exact same story otherwise. One example comes from secondary character Viletta Nu: in both versions of the story she joins Britannia's equivalent of the CIA and becomes Ashford Academy's gym teacher to spy on Lelouch. In the anime she was promoted for learning that Lelouch is Zero, as a direct result of her Easy Amnesia and Amnesiac Dissonance romance storylines in the first season; in the manga, she's Demoted to Extra and thus none of this happens, resulting in her seemingly getting the rank just because it's what the anime did.
 * It Got Worse in the final volume. The removal of some characters and plotlines led to several Out Of Character Moments. For example, Kaguya, who is Zero's biggest fangirl, is essentially the engineer behind the Black Knights' coup d'état against him and the one who smooths things over after he escapes; in effect, she takes up the roles of Diethard (who isn't in the manga) and Ohgi (whose motivation to betray Zero came from Viletta's excised storyline).
 * The Inuyasha anime has some trouble with this thanks to rearrangement of story arcs and several early episodes in which Kagome has to have a Shikon jewel shard in order to travel between the past and present through the Bone Eater's Well. Much later in the storyline, as the Jewel nears completion, there are periods in which the protagonists have no shards but Kagome and Inuyasha are both able to go back and forth through the well without difficulty.
 * In the Dragonball anime, Goku meets Dr. Flappe, a professor who lives not far from Jingle Village and was pressured by the Red Ribbon Army into creating Android 8. Several years later in Dragonball Z, the creator of the Androids (including Eighter) is revealed to be Dr. Gero. Also in Dragon Ball Z, the ship Goku uses to get to Namek is a modified version of the ship he was sent to Earth in, which Piccolo destroyed in Filler. However the latter issue is no longer present in Dragon Ball Kai.
 * Also in the Dragonball Z anime, the line from the Dragonball manga is cut where Zarbon tells Vegeta that Freeza can transform, leaving a bit of a headscratching moment when Vegeta references it later on. Kai does not fix this.
 * Anime filler shows the character Dabura becoming good. Namek's Dragonballs are then used to wish back the people who are not evil. Dabura should have been revived, yet he doesn't appear later as this doesn't happen in the manga.
 * The Garlic Jr. Saga is basically one big Adaptation Induced Plothole. It, nor any of the other movies occur in the manga obviously. It directly follows the movie The Dead Zone, which is supposed to take place before the start of Dragonball Z. If Dead Zone was canon, then there's no reason Krillin and the others don't know about Gohan in the first episode of Dragonball Z and are surprised when he unleashes his power on Radditz.
 * Plot Holes seriously tarnish what is an otherwise excellent series in Flights of Fancy, the second season of the Ah! My Goddess TV series-- Skuld is seen using her stamp power in one late episode, but there's no episode in which we see it developed, and Chihiro, and her shop, Whirl Wind, show up, but Chihiro is never formally introduced, and the fact that she wanted to start a shop is never even mentioned.
 * Flights of Fancy also inverts this Trope: Keiichi and Belldandy are an Official Couple by Episode 24 of Ah! My Goddess; at the end of the Lord of Terror arc, they share a Crowning Moment of Heartwarming when they confess their love for each other. In the 24th (and last) episode of Flights of Fancy, Keiichi spends the entire episode trying to confess his love for Belldandy, but Cannot Spit It Out-- even though Belldandy flat-out says she's ready for him to say it!
 * Hellsing: In his fight with Alucard, Luke Valentine is shown to have a strong Healing Factor, surviving after getting shot in the head by Alucard's specialized gun. However he is unable to regenerate his legs. In the manga there was no headshot. He was instead shot in the stomach by the Casull, while his legs were shot off by Jackal. In the OVA, Jackal was the cause of all three wounds.
 * In the Ranma One Half manga, Ranma (as a girl) competes with Tsubasa (who's disguise had yet to be revealed) in who can sell more food to the boys at school, but since all of them knew that Ranma wasn't a real girl they didn't buy any from her until she started wearing a disguise. However, in the anime Ranma's curse wasn't revealed by this point, so the boys bought them only from the disguised Ranma for no apparent reason.
 * Saint Seiya had one when they showed Scorpio Milo killing Shun's Master. Then the manga came out and it was . A number of Ass Pulls had to be done to fix the problem of Shun swearing revenge against someone who didn't apply the coup de grace against his teacher.
 * Doctor Slump had a story where Akane dressed up as Miss Yamabuki to play some pranks on Senbei. This took advantage of their faces looking the same. The second anime made their faces more different (And gave them different hair colors), yet they adapted this story anyway. Even though it didn't make sense any more.
 * Due to the absence of the Skull Knight (and a few other characters at that), there were a couple of these toward the end of the anime adaptation of Berserk. This partially contributed to the Cliff Hanger before the final credit roll.
 * Elfen Lied has a few. The anime begins with a violent demonstration of Lucy's immunity to bullets, despite the fact that the guards are supposed to have special bullets designed to penetrate her vectors. In the manga, she grabs a Human Shield before any of the heavily armed guards can get a shot off.
 * The anime also gave Lucy only four vectors, as opposed to the seemingly unlimited number she had in the original, while allowing her to do things she did in the manga that would be impossible with only four vectors, such as simultaneously holding a few hundred bullets in mid-air.
 * The last episode of the anime features Lucy using her vectors to block 's vectors, while in the manga, the usefulness of the hinges on the fact that vectors cannot block other vectors.
 * In the anime's Duelist Kingdom arc, it's not revealed why Bakura didn't get rid of the Ring, even though it made him evil, or even why he went to the island. The manga explains that he wants to learn the secrets of the millennium items and went to the island to talk to Pegasus.
 * And while we're on the subject, there was a filler arc in the anime that said that Duel Monsters come from an alternate world that Yugi even travels to at arc's start. They were said to have existed since about 10,000 years ago and appeared in Atlantis. When the final arc based off the final arc of the manga comes around, it's stated that There's also the issue that the Egyptian events were 3000 to 5000 years ago, not 10,000. And don't even get me started on the origins of Dark Magician Girl...

Films -- Live-Action

 * The Wizard of Oz famously combined the roles of the two Good Witches (of the North and the South), creating the plot hole where Glinda doesn't tell Dorothy what the slippers do on their first meeting, which would have saved her a lot of trouble. Originally the Good Witch of the North (not Glinda) gave her the shoes, but only Glinda knew they could bring her home.
 * On Her Majesty's Secret Service is one of the more faithful adaptations of a James Bond novel to film--which, ironically, leads to problems. In the previous novels, Bond had never met Ernst Stavro Blofeld directly, so naturally they did not recognize each other on sight in the OHMSS book. But in the previous Bond movie, Bond and Blofeld had met face-to-face. However, they still do not recognize each other in the OHMSS movie, because they didn't recognize each other in the book!
 * Blofeld had undergone plastic surgery on various occasions to change his appearance (the film even mentions this), so it is possible Bond didn't recognize him because he genuinely looked different. It's an unintentional Authors Saving Throw which makes a lot of sense in context when looked at along with the events of Diamonds Are Forever (the movie that followed OHMSS).
 * Also, both Blofeld and Bond changed actors from You Only Live Twice to OHMSS, so it also serves as a meta-joke.
 * The Harry Potter movies:
 * In the third movie, the authors of the Marauder's Map - "Moony, Wormtail, Padfoot and Prongs" - are never revealed to be, respectively. This causes problems in the later movies when the nicknames are used with no explanation. Also, it leaves anyone who hasn't read the book scratching their heads as to how Lupin knew what the map was. In turn, his worry about Sirius using the map to find Harry makes no sense for the same reason.
 * The removal of.
 * The mirror in Order of the Phoenix never makes an appearance, but a shard from it is still inexplicably a plot device in the Deathly Hallows movies.
 * The Fidelius Charm, a magical means of protecting secrets, is used twice and prominently in the books. It never shows up in the movie, leading to a lot of baffling questions about Sirius Black and Number Twelve, Grimmauld Place.
 * A minor one from the first film is how the kids get caught out of bed. For some reason they decide to go to Hagrid's house at night despite finding out about the Philosopher's Stone during the day. They have no reason to sneak out, and why would Malfoy have any reason to follow them? Does he skulk around outside the Gryffindor common room waiting for them to make a move? It's just giving them one big Idiot Ball so they can be caught and have to do detention in the forest.
 * In Deathly Hallows Part 1, the kids steal Bellatrix's wand. In Deathly Hallows Part 2, Hermione heads to Gringotts while impersonating Bellatrix and is told she needs to hand them her wand as confirmation of her identity. This very nearly blows the entire plan. What's gone is the fact that, in the book, the goblins knew Lestrange's wand had been stolen and were hoping to trap Harry's friends. Movie-only viewers wonder why Hermione didn't just hand them the wand, seeing as she had it anyway.
 * They had to make changes to Deathly Hallows Part 2 to cover for Harry not seeing, which was how he figured out where it was during the Battle of Hogwarts.
 * The presence of Cho Chang and Katie Bell in Deathly Hallows: Part 2. They are never shown to be in the same year as Harry and while the Room of Requirement is a great place for them to hide and help form a resistance, why on earth do they dress up as students and report for the roll-call? They're supposed to have graduated. Neville, Luna and Ginny were wearing their own clothes - does this mean they weren't at the roll call? Why did they not go when Cho and Katie did? Come to think of it, why did any of the students hiding in the Room of Requirement go? If they're known subversives, wouldn't they be the first to be questioned? Isn't that why they were hiding in the first place?
 * Cho and Katie are in the same year as Harry in the films' continuity. In the fifth film Cho is said to be worried about failing her OWL exams and Katie is shown in Harry's potions class in the sixth film so they're in the same year.
 * The scene explaining the taboo on Voldemort's name in DH is deleted, so it just looks like the trio either have incredibly bad luck, or the Death Eaters are fantastic trackers who don't tell Voldemort where to find Harry and inexplicably go after him themselves; and Xenophilius Lovegood is insane, but happens to have incredibly good timing.
 * This also results in an incredibly OOC moment in part 2 where Harry refers to Voldemort as "You-Know-Who" despite spending the entire series insisting on using his name.
 * A minor one, but Snitches are shown being handled with bare hands in earlier movies, despite the fact that this is later revealed to be strictly forbidden, and a major plot point hinges on it. This was a Retcon introduced in the seventh book, so they couldn't have known about that when the first movie was being made six years earlier. The seventh movie tries to tone down the plot hole by just saying that Snitches have flesh memories without explicitly mentioning that they're only supposed to be touched by the Seeker who caught them. The plot hole will still set in if you think about it enough, but at least there's not an outright contradiction.
 * In the flashback to Snape's worst memory, the part where he  doesn't affect the plot too much, but makes his character read very differently, effectively shifting his worst memory from
 * The burning of the Burrow in the sixth movie was not in the book. This contradicts events of the seventh book, when Bill and Fleur's wedding takes place at the Burrow. In the scene, Bellatrix mocks Harry about . This isn't mentioned in Seven Part 1.
 * In the fifth movie, Umbridge destroys the entrance to . This doesn't happen in the book, and it becomes a problem in the last movie when . No one bothers to explain how such a complicated magical door managed to fix itself.
 * In Infernal Affairs, only Superintendent Wong knows the identity of the undercover cop. When . In The Departed, both Captain Queenan and his assistant Sergeant Dignam know who the undercover cop is. When, the cop acts like he has no one to turn to, but . Why no one bothers to look him up is never explained. is treated as a surprise, but fans of the original would be waiting for that dangling thread to resolve for half the film.
 * In The Last Airbender, Earthbenders are kept on land, yet do no earthbending at all. In the original show the Fire Nation keeps Earthbenders it captures on a metal platform at sea, far away from the rock and ground they could use to help escape. Admittedly, both explain that the Earthbenders had their spirits broken and no longer wanted any trouble (even in the show when given access to their element the Earthbenders didn't want to fight the prison guards). It's only that the explanation for their broken spirits (no earth to bend) wasn't present.
 * The short story turned short film Paul's Case has an example of this, although it's not so much a plot hole as a moment of characterization kept in when it didn't fit with the other changes. In the original story, Paul is portrayed in a way that makes it easy to assume he has mental problems. In the film he's turned much more sympathetic, and is shown to be a victim of circumstances, yet the film keeps in a scene where Paul creepily fantasizes about his father shooting him when he crawls through his basement window.
 * Watchmen in graphic novel form has a scene where Silk Spectre starts a fire on Nite Owl's plane while looking for a cigarette lighter. The movie adaptation keeps the scene. But while smoking hadn't disappeared in the rough quarter century between them, it had become largely verboten in the movies, so Laurie just pushes buttons for no reason.
 * There is also a scene copied from the comic where Laurie sees Dr. Manhattan and says she heard he was on Mars. He was, but in the movie there was no way for her or anyone to know. The scene where Dr. Manhattan tells a soldier he's leaving for Mars doesn't appear in the movie, he teleports from the studio to the abandoned base, then straight to Mars.
 * In the film of Voyage of the Dawn Treader, a search for seven swords is superimposed over the novel's search for seven missing Telmarine lords. The claim that at least one of these swords was given to Caspian's father by Aslan is an Adaptation Induced Plothole: Aslan hadn't been seen in Narnia for centuries prior to the events of Prince Caspian, and as a Telmarine, Caspian's dad would've been brought up to believe "Aslan" was either a myth or a monstrous lion-demon, not a benefactor.

Live-Action TV
"Crow: "For those of you following at home, Rita is dead.""
 * Mystery Science Theater 3000 had on-and-off trouble with this, due to the format of the show: they had to trim out questionable content and pare down the films they riffed so that, in combination with the host segments, the show would only fill roughly 90 minutes of run time (in a two-hour time slot). The show's staff stressed that they tried not to artificially add to a film's poor quality with their edits, but it occasionally happens.
 * The catastrophic Joe Don Baker vehicle Mitchell was 97 minutes long, but was cut down to 70-75 minutes. One of the things cut out was the death of John Saxon's character Mr. Deaney, one of the film's primary antagonists. This prompts Joel to rather unfairly riff, "Wasn't John Saxon in this movie?"
 * This was actually averted in Sidehackers. One of the scene that had to cut out due to content involved the hero's girlfriend being brutally gang raped by the antagonist and his lackeys, ultimately ending in her death. In order to explain why the main heroine suddenly disappears halfway through the film, one of the bots makes the following remark.


 * The Movie also cuts some exposition from This Island Earth.
 * The TV adaptation of Going Postal skips the subplot about what happened to the previous postmasters by revealing they were killed by Reacher Gilt's banshee assassin. However, the only reason the Post Office is standing in the book is that Gilt doesn't see it as a threat; as soon as he does, he doesn't mess around killing postmasters, he burns the place to the ground. In addition, a rearrangement of scenes means that TV Gilt has to  personally, when the man is visiting his office, rather than employing the hard-to-track Mr Gryle to swoop down and  . Despite the TV version retaining Ankh-Morpork's capable and determined Watch (and its bloodhound-like werewolf), this crime apparently goes unsolved.
 * Talking of the Watch, Angua twice arrests Moist for breaking his parole by leaving the city, but for some reason there was no problem earlier when he took a horse to Sto Lat. (In the book, it's made clear he can leave the city as long as he's on Post Office business, which applies all three times.) It's also not clear why this is even Angua's job; Mr Pump is still his parole officer, and collects him when he actually tries to escape.
 * In the TV adaptation of A Game of Thrones, they re-tell the introduction story of some Night's Watchmen being ambushed by the Others, a race of undead killers. Both the TV series and the book end the scene with the POV character coming face-to-face with a monster. In the book, only the Night's Watchman who stayed behind manages to survive the incident. In the TV series, however, the only survivor is the POV character, with no explanation of how he escaped his close encounter.
 * In season two, the subplot of Sansa working with Dontos Hollard to escape King's Landing is cut, and when Sandor offers to take her with him, he's far less creepy about it. Yet she still refuses, for no apparent reason.
 * In The Worst Witch Cackles Academy has a fair share of teachers that aren't seen and don't come into the story that much but the TV series shows that there are only four teachers at the school - Miss Cackle, Miss Hardbroom, Miss Bat and Miss Drill - yet in the second season a Miss Gimlett is mentioned as being the Year Head for the 2nd year girls but has moved away over the summer. Miss Gimlett was never mentioned or referred to before that episode and apparently never used the staff room. In the books we didn't know what Miss Gimlett taught since the only lessons the girls were ever shown having were potions and chanting but the TV show has Miss Cackle teaching spells and no other subjects, apart from PE so that begs the question what did this elusive Miss Gimlett teach before she left?

Tabletop Games

 * More of an edition change induced plothole, but in the Dungeons and Dragons 3.5 player's handbook, a priest of Pelor, the quintessentially good deity of Greyhawk, is seen using a Symbol of Pain spell, which good aligned gods cannot grant. What happened was that they reused some artwork from the 3.0 PHB of the priest using the pain aspect of the Symbol spell, which was originally an unaligned spell.
 * This, along with other artwork of said cleric being a dick to his party, resulted in the creation of Pelor the Burning Hate.
 * For that matter, did they ever explain how Drow society in Forgotten Realms - which was based off of infravision - functioned in 3.5 - which removed infravision? They kept time through a giant rock pillar that had a "heat" spell cast on it, for pete's sake.
 * The original CD&D supplement for the Mystara setting's nation of Karameikos included a three-paragraph summary of the content of an epic poem, roughly equivalent to the real-world Iliad, that underpins much of the native Traladaran culture's history and religion. When Karameikos was re-packaged for an AD&D audience, the three-paragraph summary was presented as the actual saga, meaning it was no longer a poem, no longer exciting, and no longer appealing enough to justify the Traladarans' having revered it for hundreds of years.

Videogames

 * The Warriors video game, in lieu of changing the story of the film, opted to make most of the game a prequel depicting the Warrior's rise before the events of the main story. For the most part, it works. However, there is one scene where Masai demands to know who The Warriors are and none of the other Riffs can answer him. In the film this makes sense, since we have no reason to believe the Warriors ever did anything to stand out. In the game however, the missions involve fighting their way through several gangs (trashing dozens of members with only four, at most, of their own), beating up or killing several other gang leaders and overthrowing the rival gang of Coney Island who they split from. While the Riffs ARE the biggest gang in the city, and presumably don't follow everything that happens with the small-time gangs, it is strange to think that none of them would've heard about the Warriors given all the havoc they cause.
 * In Metroid Prime Trilogy, the help for the combat visor in the first game notes that the visors you possesses are indicated in the lower left of the screen. This is not true for the trilogy version where they are in a separate menu accessed by holding - and selecting the visor from a menu, and only the current visor remains listed on the HUD.
 * Another example, from the same game (also from the North American re-release of Metroid Prime). In the original release of Prime, Metroid Prime had been captured by the Space Pirates and studied for a while. Then, it broke out, merged with some Pirate gear, and escaped back to where it came from. The problem is that where it came from was supposed to be behind an impenetrable barrier that you spend most of the game getting the key to. So this was changed in the re-releases to fix the plot hole; it was never captured by Pirates and so forth. However, in so doing, they introduced another plot hole: if the Metroid Prime never was captured by the Space Pirates, where did it get all that fancy Pirate gear that it uses on you in the first battle? And why is it even called "Metroid Prime" since it was the Pirates who gave it that name?
 * The second stage of Turtles in Time, "Alleycat Blues", takes place in a back alley in broad daylight. This isn't a problem for the '80s Turtles, who moved around freely during the daytime, but their Mirage comic and 2003 incarnations generally stick to nighttime activity - so when the game was remade as Turtles in Time Re-Shelled, using designs from the 2003 cartoon...
 * A plot hole created between platforms of The Fancy Pants Adventure: World 3 appears in the Canopy Forest level. There is a squirrel on a balloon who gives a minigame challenge, and reward the player with "a squirrel-y prize". In the console versions of the game, that prize is an acorn-shaped hat, while in the online Flash version, it's a rather nebulously relative pair of green pants.

Western Animation

 * In the Ellipse-Nelvana Animated Adaptation of Tintin, Some of the dialogues shows that The Calculus Affair took place before the moon stories (Destination Moon and Explorers on the Moon) instead of the other way around like in the original comics. However, in The Calculus Affair we see Tintin and Haddock fought off both Syldavians and Bordurians to rescue Professor Calculus. Yet in the moon stories, we see Calculus happily working for the government of the country who kidnapped him (Syldavia).
 * In The Smurfs original comicbooks, it has been established that Grouchy Smurf was the Smurf who was bitten by the Bzz Fly in "The Black Smurfs", and his current moody behavior was caused by this (either due to having been more time as a Black Smurf as the others, or because he was directly stung by the fly, while the others were bitten by their infected peers). The Hanna-Barbera Animated Adaptation had several episodes that included Grouchy Smurf (as grouchy as ever) before adapting this story into "The Purple Smurfs", so his behavior is unexplained.
 * It cannot even be excused by Anachronic Order, since Lazy Smurf is the one bitten by the Purple Fly, and it's shown later when Grouchy Smurf is bitten by a Purple Smurf, even telling at mid-transformation "I hate... GNAP!"