Opening a Can of Clones

In Speculative Fiction, Shape Shifters, robot duplicates and clones are exciting and can add a layer of ambiguity and suspense to a story. It will fill characters and viewers with paranoia and make for great shocking revelations. However, they can also completely derail said story and kill all drama when fans get lost in the forest of Epileptic Trees. The problem stems from the possibility that if clones, shape shifters, time travelers or body hopping aliens can make and unmake plot points at whim, how can viewers be sure that a given story element is "real?"

The reasoning here is similar to how a setting where Death Is Cheap takes away dramatic punch from future character deaths. By allowing for the existence of these duplicates the author basically has a huge Reset Button with giant neon lettering spelling out "Wanna bet this dramatic revelation, death or plot twist is here to stay?" These fears can be confirmed if an author starts Ret Conning events or casually undoing changes using these tropes.

It's not that the tropes are bad, but that they bring with them a latent threat that has to be defused quickly or risk distracting viewers or damaging Willing Suspension of Disbelief. Perhaps clones dissolve once killed; so if Alice leaves a corpse, then by golly she is dead. Of course, a story with clones or what not may never fully dispel some Wild Mass Guessing (even with Word of God), but hey, fans like tinfoil hats.

A few things that may cause this reaction:
 * Death Is Cheap via Expendable Clones.
 * Overuse of the First Law of Resurrection inevitably makes any death suspect.
 * Poor use of the Cloning Gambit.
 * Revelation that what you killed was Actually a Doombot

A few ways to avoid this reaction:
 * Ambiguous Clone Ending -- Here the intention is to keep the audience guessing, rather than a side effect.
 * This Was His True Form -- If the shape shifter reverts to their default form, then reviving a dead character this way is impossible.

Also related to All the Myriad Ways and the Second Law of Metafictional Thermodynamics.

Anime and Manga

 * Played with in Battle Angel Alita: Last Order, with all the Desty Nova and Gally/Alita clones. Yukito Kishiro basically runs with the Brain Uploading and turns it into as ridiculous a situation as he can manage.
 * How ridiculous?
 * Used to a very confusing effect in Tsubasa Reservoir Chronicle. Some are aware of being one, others are not, but given all the alternate world versions of characters, cloning, and lineages, it can become very hard to follow.
 * Blue Drop: The Emul Force allows the user to project his/her thoughts, creating living sculptures. It's used as a decoy countless times, and every major character death gets unsurprisingly undone this way.
 * Naruto provides an example of this, which was clearly an Ass Pull in response to negative fan reaction. Several chapters after is seemingly killed, he is revealed to be alive, with what actually died having been a clone  - even though this contradicts all previously established facts about clones. Though  clones are very different from every other type.
 * Near literally done in the Elfen Lied manga with a squad of four Mariko clones.

Comic Books

 * An Astro City story has a defense lawyer get a gangster acquitted for murder by invoking this trope, citing incidents involving Evil Twins from parallel universes and shapeshifting supervillains.
 * From the X-Men:
 * Professor X apparently dies during a battle against Grotesk. Later it's revealed that the Changeling had been masquerading as Professor X at Xavier's request.
 * Phoenix (Jean Grey) apparently kills herself so she can't go Dark Phoenix again. It later turns out to have been the Phoenix Force impersonating the real Jean Grey.
 * Marvel Comics' S.H.I.E.L.D. has something called LMDs: Life Model Decoys. Whenever Nick Fury dies don't worry, it was an LMD. Then he got Killed Off for Real; but it eventually turned out that was an LMD too. (The writer of his funeral, aware of this trope, wrote the characters responding with amused disbelief and then had Wolverine turn up specifically so his Super Senses could confirm it was the real deal...but however you may try, there's just no stopping the First Law of Resurrection.)
 * Dr. Doom has the same deal. Any defeat - or anything else that someone wants to consider Fanon Discontinuity - can be handwaved as Actually a Doombot.
 * A running joke around the time of Secret Invasion is that when a character in Marvel is out of character, it was a Skrull impersonator.
 * Honestly, this has become so much the norm for comics that almost NO death is taken seriously, with fans almost immediately asking "Well, how long before they come back?" whenever someone dies. As early as 20 years ago, a number of characters in-universe in the X-Men titles would joke that "mutant heaven" didn't have pearly gates but revolving doors, and for years it was a common saying among comic fans that "No one stays dead except Bucky, Jason Todd, and Uncle Ben" (and it's worth noting that two of those three are now alive again themselves...).
 * Recent storylines in both major companies (Blackest Night, Secret Invasion, Necrosha) have done absolutely nothing to dispel this mentality, as dozens of formerly dead characters are now alive again. DC claims that Blackest Night has closed the door to future resurrections, but very few fans seem to be buying it.
 * Thanos, the Jim Starlin created Big Bad in the Marvel Universe, has clones called Thanosi that Starlin can use to explain away any defeats that Thanos might suffer (which, purely coincidentally, are almost always written by writers other than Starlin). Starlin has even gone so far as to say that not even omnipotent cosmic observer the Watcher can tell the difference between a Thanosi and the real Thanos.
 * Skrulls did it. To the entire Marvelverse. Lampshaded when Spidey complains that he had clones way before everyone else was getting replaced by Skrulls.
 * Lampshaded in the Star Wars Expanded Universe with Dark Empire. Basically every time Luke kills a Palpatine clone, he transfers his soul to another clone. Luke pretends to go over to the dark side and is ultimately on the dark side.

Literature

 * Philip K Dick loved to play with this sort of idea. Several of his stories feature duplicates that are so real that even they don't know they are duplicates. It's confusing and Paranoia Fuel and his fans wouldn't have it any other way.
 * Greg Egan extensively Zig Zaggs this trope in virtually all of his stories, which frequently feature future humanities where people variously are, a) robots, or b) disembodied software. Moreover, because of this, many of his characters experience what amounts to an ambiguous form of Immortality in Cyberspace, and variously either die, kill themselves, or fail to die for huge tracts of time without seriously derailing storylines they're part of.
 * Additionally, many stories feature large numbers of copies of the same characters who gradually grow apart into independent people over the course of the storyline, or simply provide multiple redundancy when characters need to do many things at once, or are likely to die in the doing of something plot-related.
 * A slight variation on the trope has begun to appear in A Song of Ice and Fire with the Faceless Men, an order of assassins who can perfectly imitate just about anyone. This has lead to a lot of fan speculation; the only Faceless Man we've really been able to track is . Theories now abound as to who might be a Faceless Man, with contenders including, and many, many, many more.

Live Action TV

 * Alias introduced cloning in the form of "Project Helix", a process by which identical Doppelgangers of people could be produced. The first double was a one-off character, but the second double was a complete shocker:  The double was a very unique twist . . . at first. Then, they brought back the double-switch when , again later in season four when it was revealed that   and again in season five when  . It got to the point where a common saying in regards to the show was "they're not dead even if we've seen a body - it's probably a clone".
 * Battlestar Galactica got hit with this right from the bat. Even though there were only 12 Cylon models, you could never be quite sure which version of the model you were talking to. Especially the Sixes and Eights:
 * Number Six: Caprica Six, Head!Six, Gina Inviere, Natalie Faust, Shelly Godfrey, the Six on the Armistice Station, LabCoat!Six, the Six who headed "The Farm", the dying Six on the basestar, Lida, Sonja, and Prostitute!Six from "The Plan".
 * Number Eight: Sharon "Boomer" Valerii, Sharon "Athena" Agathon, the Eight on Ragnar, WhiteCoat!Eight that Athena kills, the many naked tai chi Eights, the dying Eight on the basestar, the unplugged!Eight Anders talks to, the dying Eight Saul Tigh forgives, the Eight who resurrects D'Anna, Cynical!Eight from "Face of the Enemy", Sweet!Eight who betrays Gaeta, and the Eight who.
 * Misfits started to suffer from this in the second season, as Curtis has the ability to rewind time if he feels enough guilt towards something that has happened, giving him a chance to Set Right What Once Went Wrong. So when the Misfits Discard and Draw new powers during the Christmas Episode season finale, the show explicitly removes this power from play.

Web Comics

 * Darths and Droids notes the wasted potential that the proven existence of shapeshifters has in the Star Wars saga in the commentary of one strip.
 * And again with shapeshifters and clones in an outtake strip.
 * ~The Adventures of Dr. McNinja~ cleverly avoids this problem by having all of the cheap clones of Doc that commissions be flawed and eventually disintegrate. However, there's one original clone left over, raising the stakes on the Like You Would Really Do It cliffhangers that the author frequently employs.

Web Series

 * In the French Web Serie Le Visiteur du Futur, the Dr. Henry Castafolte has been duplicated many times by creatures between clones and robots. The only way for them to find out what they really are is to see The Bar Code Tattoo on their arm.

Western Animation

 * Frequently Lampshaded in The Venture Brothers whenever it is revealed that.
 * This also explains why they give the impression of having been dropped on their heads several times as babies-
 * Up until the finale of season 3,
 * Gargoyles' creator Greg Weissman tells in Ask Greg of how his children thought Elisa was acting bad in the episode "Protection" because it was a clone, given that an earlier episode had introduced a clone of Goliath (she was actually pretending to be a corrupt cop to fool a mob boss).
 * At least in the show itself they avoid this by having clones be a Palette Swap of the originals instead of an exact physical match.
 * Futurama's season opener "Rebirth" opened with the entire cast except Prof. Farnsworth being mutilated in a horrible shipwreck. Farnsworth dumps the remains into a vat of "adult stem cells harvested from perfectly normal adults whom he killed for their stem cells" and reincarnates his entire team. Later, after most of the episode was centered around Cloning Blues via a robot double of Leela, it turns out that wasn't really reborn, but is actually a robot double himself.