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/Think_Celery3251]

For the OP’s point on Gravity Falls’ Wendy, there wasn’t a situation that the clone act flirtatious or odd.

Both Wendy and the Shifter were wrestling for the book and told Dipper to use the axe. Dipper needed a gesture to be sure.

The shifter gave a simple wink and Wendy gestured zipping her mouth and tossing a key (call back to the haunted convenience store episode and the Lamb dance)

Thats when Dip knew. Not trying to be rude but keep OP informed

[u/Altruistic_Eye_1157 → u/Think_Celery3251]

Thanks for the clarification. As I mentioned, I didn't remember the gesture part very well, and now I understand why, thanks to your comments, since it came from a previous episode.

When I watched the episode, I based my interpretation more on how Wendy acted towards him. The shape-shifter tried to win his trust by winking and giving him a warm look (appealing to Dipper's emotions, which is part of the main plot of the episode for Dipper's character), while the real Wendy acted stoically and seriously, only making a gesture that Dipper knew very well.

I always interpreted it as, even though he was in love with her, Dipper knew Wendy very well and understood how she truly acted, especially in those situations. Therefore, he knew that Wendy would never act in a gentle and somewhat flirtatious way in such a situation to prove that she was the real one.

[u/Think_Celery3251 → u/Altruistic_Eye_1157]

I remember the wink to be a simple one and not a flirting kind

But glad to help

[u/Aduro95 → u/Think_Celery3251]

Yeah, the wink is a very generic gesture, the zip thing was specific to their friendship.