Phlebotinum Breakdown

Things break. This is just a natural rule of the universe. Even the Green Rocks are going to fail to work at some point.

Of course, this is fiction, so when your Applied Phlebotinum breaks down, it is always going to do so at the worst possible minute. Or, to quote Dark Helmet: "Even in the Future, nothing works!"

What's worse is this: real things that you may have encountered in your daily life often break. When they do, they either function at a reduced capacity or not at all. This can happen on TV, but it is at least as likely that, rather than simply not working, they will do something else entirely, perhaps even something more spectacular than the thing they do if you Reverse Polarity.

The thinking is this: the transporter does something really amazing and miraculous when it's working. Just imagine how amazing and miraculous a thing it could do if it were broken. Never mind that this is no more logical a line of thought than, say, "A functioning toaster makes toast, but a broken one might start suddenly making French toast! Or maybe even sausage links!!"

Fortunately, if it's Tim Taylor Technology, you can usually fix it by applying more power. Unless it's vulnerable to Phlebotinum Overload, that is... then something will Go Horribly Wrong. If you're really unlucky, it'll work fine up until when you need it most.

Holodeck Malfunction is a subtrope.

Anime and Manga

 * The "malfunctioning toaster would make sausage rule" also applies to magic as well as science. In Yu-Gi-Oh! GX, when Saiou's defeat-equals-mind-control spell fails on Judai, instead of just not being Brainwashed, Judai loses the ability to see monster spirits and the images on Duel Monsters cards.
 * Kurau in Kurau Phantom Memory suffers from bouts of weakness since the arrival of her "pair", Christmas—usually when being chased or having to fight. Of course, when Christmas is around it only adds to her strength.
 * End of Evangelion. Asuka. Final fight. Power shortage.

Film

 * The entire purpose of the Millennium Falcon in Star Wars?
 * Not really, it only actually breaks down in Empire Strikes Back, the rest of the time it just 'looks' like it's going to happen.
 * Quite the opposite, actually. According to every standard, a ship that tampered should be very fragile, but actually, she has negligible problems when blasted.
 * The only reason the Falcon was having problems in the 2nd film is because Han had taken the opportunity of landing in a secure hidden stronghold to take the ship apart for maintenance. The arrival of the Imperials forced him and Chewie to put it all back together as best they could.
 * At the end of Short Circuit 2, Johnny 5 tries to use his radio that hacks into things on a boat, but it doesn't work because the boat is not electronic.
 * In Clockstoppers, Zak's hypertime watch malfunctions after getting wet.

Live Action Television

 * The transporter in Star Trek would break (in the simple "fails to work" sense) pretty much any time our heroes needed to make a hasty exit from a hostile planet. It would break (in the spectacular sense) on occasion as well. Broken transporters have created twins of at least two people (Kirk and Riker), in one case somehow separating "good" and "evil", caused people to regress in age, merged two individuals to create a viable and integrated third individual, sent people to a parallel universe, and even transformed a bunch of people into manatees trapped in the void between dimensions.
 * Star Trek's holodeck is also a prime example. The most common "simple" breakdown is to lock the senior officers inside and turn off the safety protocols. Why these features would always be the first to break defies explanation. However, the holodeck too can malfunction more extravagantly, say, by giving a simulation of Professor Moriarty full sentience and complete control of the ship's computer.
 * Strictly speaking Moriarty wasn't a malfunction; the holodeck was working entirely correctly when it created him. The problem was incompetence on the part of the user, Geordi LaForge; a 24th-century PEBKAC, if you will.
 * Well, if a misspoken word causes the holodeck to create a fully sentient criminal mastermind, it is fair to say there are also some serious design problems.
 * In fact, most Star Trek: The Next Generation plots revolved around some form of this, from malfunctioning replicators to crew members devolving to the everyday, run of the mill warp core breach.
 * Darths and Droids actually points this out regarding the "warp speed limit" and links this Trope's page.
 * And the holodecks. And Data. Both of them should have tossed off of the 1701D at their first sign of major trouble... which happened for both of them in TNG's first season. As we have Plot-Driven Breakdown (wherein the breakdown is part of the plot developement) I wonder if these cases shouldn't be under a new category: Breakdown Driven Plot, cases where the breakdown isn't simply a plot complication, it creates the plot from whole cloth.
 * In a more down-played fashion, the communicators more than once had to be kept from working properly for the reasons mentioned in the Can You Hear Me Now? trope.
 * Stargate SG-1 frequently has DHDs broken or destroyed on planets where the team would not like to stay. More extravagantly, a malfunctioning Stargate trapped one of the team in a wormhole (when one Stargate was destroyed), trapped Earth in a time-loop (when working in conjunction with an alien device that was intended to do this), nearly destroyed a star (though technically the gate was not malfunctioning, just being abused), actually destroyed a star (this time on purpose), sent SG-1 backward in time, and almost sucked Earth into a black hole. The worst the gate has yet done on Stargate Atlantis was to ensnare a puddlejumper when one of its engine pods failed to retract.
 * Not mention the teleportation chips SG-1 had installed recently for purposes of whenever deus ex machina is needed. Take a wild guess what happens when the episode is 30 minutes in and one is not needed.
 * Recently in Stargate Atlantis the Stargate managed to send Colonel John Sheppard 48000 years in the future by the same problem that sent SG-1 to the past, considerably increasing the bar for Stargate Atlantis' Stargate malfunctions.
 * It wasn't an actual malfunction on the part of the stargate, just an unlucky (or lucky given the outcome) event, and a rare one at that (it took 800 years or so for another event to occur). The ancients' seem to be noticeably lacking in their forethought on such issue.
 * Also, in one try at making a power source more powerful than the Zero Point Module (a device that draws energy from an artificially created micro-universe) in Stargate Atlantis they ended up almost destroying a parallel universe (although they knew something as such would happen, they only didn't knew the other universe would be populated, much less that it would be a parallel one). The incredible part is that the machine became an actual extra-dimensional portal.
 * The gates etc. don't act up as much in Atlantis because the main characters are doing enough on their own.
 * This is actually at least partly justified. The main Stargate lacked its standard control system, a DHD, and instead had a jury-rigged human-made one using supercomputers. This meant they could easily bypass safety systems, but it was also more prone to malfunctioning in plot-moving-along ways, such as in "Red Sky" where the wormhole pierces through a sun and damages it.
 * A particularly bad offender was Seven Days, where the sphere seemed to malfunction more often than it functioned, and could do anything from inverting the morality of the entire universe to turning its pilot into (I swear ) the pope.
 * Doctor Who's TARDIS is a particularly unreliable bit of Phlebotinum. Its navigation is notoriously unreliable when it works at all, its camouflage system has been stuck for the past 40 years, it has a habit of ignoring the Doctor's directions to deposit him in situations of extreme and immediate peril, and it was once blown to bits outright. Also, it once shrank its passengers to the size of fleas. In contrast to the examples above, though, rather than breaking at the worst possible moment, the TARDIS seems to work correctly only when it's absolutely vital that it does (see Million-to-One Chance, One Buwwet Weft). That said, the TARDIS is supposed to be piloted with six crewmembers, not just the Doctor plus one.
 * It's heavily implied that when the TARDIS lands in the wrong time zone/place at the start of an episode, it's because the Doctor just doesn't care that much. It's shown that the TARDIS making that noise is the Doctor intentionally flying it badly. This explains why it goes where it needs to at critical moments. The rest of the time he's effectively showing off to the companion, like your mate who drives with two fingers on the wheel and never uses the footbrake.
 * And he flies it with the 'parking brake' on.
 * Apparently so does every other Time Lord we've ever seen, since all TARDISes have been shown to make the same sound.
 * The episode "The Doctor's Wife" revealed that the TARDIS, and it often sends the Doctor where thinks he needs to be, sometimes malfunctioning to keep him there.
 * In Voyagers, the boy visits the time of Thomas Edison and finds to his horror that the curious inventor has disassembled his time machine, the handheld device called the Omni. The inventor insists he is confident he can reassemble it, and by the end of the story, he proves it, as he presents the boy with a fully intact Omni.
 * Also, the Omni malfunctioning is what starts off the series; it's not programmed to take Bogg past 1970, but a brief malfunction lands him in 1982, where he picks up Jeffrey...who he then can't take home again.
 * Pick ANY show which features ships with some FTL drive. Then get the ship in some deep shit where jumping out (then optionally coming back with reinforcements) would be the best option. If the ship has been hit, it won't work. Sometimes justified with some technobabble about the structural integrity and the massive forces of hyperspace. Sometimes not. Notable occurrences:
 * Star Trek and every incarnations.
 * Star Wars, the Millennium Falcon's hyperdrive is a trope to itself.
 * The only time the Millennium Falcon's hyperdrive malfunctioned (not due to battle damage) was when it was purposefully disabled by Imperial forces. Even then, one astrodroid was able to bring it back online in moments.
 * Farscape
 * Stargate SG-1 and Stargate Atlantis
 * In the Wizards of Waverly Place episode "Fashion Week", the magic power plant went offline, and the wizard spent almost an entire episode without magic.

Tabletop Games

 * Warhammer 40,000 likes this one, usually with things (or people) breaking or being corrupted by Chaos at just the right time to sentence lots of people to horrific death.
 * Paranoia likes this one, usually with things (or people) breaking or being sabotaged by Commie Mutant Traitors at just the right time to sentence lots of citizens to highly amusing death.

Video Games

 * In Fallout 1 the water chip of your home vault breaks (replacements were shipped to another vault, of course), starting your quest for a new one. Although Fallout 2 reveals the cause of the water chip failure:
 * At one point in No More Heroes, an enemy sets off the sprinklers when he sees Travis coming. The water shorts out his beam katana's battery, and a segment follows where Travis, being electrocuted, must run a gauntlet of enemies to reach the room with the sprinkler controls. Even after the sprinklers are turned off, you have to recharge the katana, though the game does give you a Full Battery power-up.
 * In the PC game Star Wars: Empire at War - Forces of Corruption, during the last mission, Tyber Zann captures the Eclipse-class Star Destroyer. The game then allows you to use its superlaser, capable of smashing a capital ship instantly. Predictably, it breaks down just as a Super Star Destroyer enters the area.
 * Even worse, since you're expected to defeat both the Imperial and Rebel forces at the same time.
 * The superlaser does come back online but only after the Super Star Destroyer is blown up, leavjng only a few cruisers and frigates to finish off. And then, Zann goes ahead and blows up the Eclipse instead of keeping it.
 * Unreal was a bit inconsistent with this, human tech either worked far better than it should or very badly. In one case a futuristic communicator didn't work on a ship about hundred metres away, sensors are mentioned as being infective but other cases have weapons working underwater and signals getting off planet. The invading aliens however, have no problems getting their stuff to work.
 * At the end of Descent 2, the Pyro GX's warp core malfunctions and dumps him in the wrong place.
 * Later revealed in Descent 3 to have been deliberate sabotage.
 * At the end of 'Halo 3'', the firing of the replacement Halo causes the slipspace gate to collapse prematurely, dropping MC and Cortana near a Forerunner planet in an unknown location.
 * In Mega Man Battle Network 3, Flashman's last gasp before deletion glitches up Lan's PET, at one point making it impossible for Megaman to jack out.

Web Comics

 * Discussed about in this Darths and Droids strip, with link to this page.
 * Parodied on Bob and George, specifically the Star Trek "holodeck malfunction". After the training simulator breaks and traps someone inside a deadly simulation, they ask if this happens often. They learn that this has happened every single time they use it. And they keep doing it anyway.
 * The TF Gun in El Goonish Shive sometimes seems to break after being used. One instance was a bit of a Noodle Incident, while two others led to a major story line.
 * In Impure Blood, the timepieces are silent, giving no warning.
 * In D and DS 9, after an attack by the Borg (and a Critical Hit roll) the U.S.S. Saratoga suffers a Warp Core Breach. This happens less than one minute into the campaign.

Western Animation

 * Futurama spoofed this in "Kif Gets Knocked Up a Notch" by having a holodeck malfunction bring the greatest villains of history to life: Attila the Hun, Professor Moriarty, Mr. Hyde, and "Evil Lincoln". In an homage to Star Trek, Moriarty declares, "Righto gents, it's another simulation gone mad, murder and mayhem, standard procedure."
 * Parodied in a "Treehouse of Horrors" episode of The Simpsons, where Homer's toaster turned into a time machine when he attempted to repair it after smashing it trying to get his hand out of the thing.
 * Ben 10 has this at least once every episode. Handy viewer shorthand: When the Omnitrix is red, Ben can't transform because it needs to recharge. Also, there was one of the "toaster makes sausage" variety, where prying off the faceplate of the Omnitrix with a screwdriver and trying to stick it back on with bubble gum results in that episode's transformations becoming Biological Mash Ups.
 * Codename: Kids Next Door: The origin story behind the Delightful Children From Down the Lane goes that Father's first Delightfulization Chamber malfunctioned and overloaded when he put the five of them inside, turning them into a kid-hating zombie hive-mind rather than "the perfect children."
 * Either despite or because of being set in Detroit of The Future, the (nonsentient, Earth-made) robots in Transformers Animated tend to break down quite a bit. Especially around Captain Fanzone. This would mark the Transformers as superior beings, if only the space bridge would stop exploding.