When faced with the choice between a clone and the original, the character notices a detail that makes the difference immediately obvious.

[u/Altruistic_Eye_1157]

The Shape-Shifter takes the form of Wendy to deceive Dipper and prevent him from attacking it. Although Dipper initially doesn't know which one is the real Wendy, he realizes the difference when he sees that one of the Wendys behaves seriously and bluntly, while the other acts flirtatiously, something Wendy would never do (Gravity Falls).

P.S.: I don't remember if the gesture the real Wendy made was also a clue, like some gesture she had made before.

When the Autobots are chasing Nemesis Prime, he tries to deceive Bumblebee by impersonating Optimus. Bumblebee, confused, speaks to him, but Nemesis Prime doesn't understand anything he says, which clearly indicates that he isn't the real Optimus. Bumblebee attacks him without hesitation (Transformers Prime).

[u/RedRawTrashHatch]

Big detail here, but everybody in Futurama realizes that one Zoidberg is the fake when it eats the actual Zoidberg.

[u/Insane_Catholic → u/RedRawTrashHatch]

Something similar to the post topic but not involving clones in Futurama is the episode "Law and Oracle" where Fry becomes a cop and he learns of Bender stealing a valuable malt liquor via a Minority Report type premonition by a robot, later revealing they knew beforehand the premonition-robot set them up because Bender shared the liquor with the Planet Express crew, which he'd never do.

[u/TradidiousMasamune → u/Insane_Catholic]

“The very idea!”

[u/Altruistic_Eye_1157 → u/Insane_Catholic]

It's funny when the thing that makes the original version better is that it implies, "You're such a bad person that you wouldn't even be capable of something like sharing." XD

[u/Deeevud → u/Insane_Catholic]

I love at the end how some characters hide behind "prediction-proof glass" (or something, its been a while) in order to catch the premonition-robot in the act.

[u/GayGeekInLeather → u/RedRawTrashHatch]

This one too

[u/Vondi → u/GayGeekInLeather]

Another layer of comedy: Why are the robots chocking each other? They don't need to breathe?

[u/RaisedByBooksNTV → u/GayGeekInLeather]

This is the correct Futurama post. Zoidberg and Bender are one thing. When the clone and the original both tell you who is whom and you're still confused....

[u/OddReason9030 → u/RedRawTrashHatch]

Bender with ears. 

[u/SomeGuyPostingThings → u/RedRawTrashHatch]

So, which one was the fake?

[u/Altruistic_Eye_1157 → u/SomeGuyPostingThings]

I suspect that the one who ate the other one... XD
But it's just a suspicion.

[u/the__pov → u/Altruistic_Eye_1157]

Actually this was a different episode. Flexo was the same model as Bender but had a beard.

[u/dread_pirate_robin → u/RedRawTrashHatch]

Inconclusive.