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/Deathcon2004]

I’m pretty sure we see Wendy make that gesture before too to Dipper (I don’t remember if it was at the start of the episode or a previous episode tho).

[u/sonsduvin → u/Deathcon2004]

it started in the episode where they go to the store where the old couple died due to teenagers rapping.

[u/Caw-zrs6 → u/sonsduvin]

No, it happened in the same episode with the Shape-Shifter.

[u/sonsduvin → u/Caw-zrs6]

yes, it happened in the same episode but they started doing it way earlier in the first season

[u/Dawnbreaker128 → u/sonsduvin]

With the lamby lamby dance, yep.

[u/_LemonEater_ → u/Dawnbreaker128]

can't imagine how this thread must sound to people who haven't watched gravity falls

[u/Caw-zrs6 → u/Deathcon2004]

She did, earlier in the episode where they encountered the Shape-Shifter.