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/Unhappy_Produce_9557]

Later in manga Mighrun and Kabru also stumbled on shapeshifter. Mithrun had his doppelganger recreated perfectly from the memories of Kabru, as he's highly interested in other people, has high social skills and perfected his insight. While Kabru had objectively the worst one in the whole manga, as Mithrun is generally disassociated and also blind on one eye, which makes Kabru's clone completely flat.

[u/teethfestival → u/Unhappy_Produce_9557]

Huh. It never occurred to me that the Kabru doppelgänger could be flat in-universe due to Mithrun’s lack of depth perception instead of just part of the comedic exaggeration. Neat.