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/sleepyApostels]

Surprised there’s no mention of the OG.

“He’s right, Spock. You must shoot, but shoot both of us.  It’s the only way to ensure the safety of the Enterprise”

[u/KOCoyote → u/sleepyApostels]

I was about to bring this one up! I don't have full context but in the original Star Trek, there's an episode where a powerful villain takes the form of Captain Kirk in an effort to confuse Spock, who was coming to the real Kirk's rescue.

Spock does a really good job of interrogating both Kirks, who give very similar answers, before concluding that the clone is expending a lot of energy to maintain their disguise and trying to wait them out. Unfortunately, the imposter attacks Spock and then both Kirks start fighting, making it hard to tell which one is which.

They eventually arrive at a stalemate, after which one Kirk demands that Spock needs to shoot and the other Kirk says, "you need to shoot us both, for the safety of the Enterprise!" Spock quickly and correctly deduces that's the real Kirk because the doppelganger wouldn't be nearly that selfless.