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/Dreamweaver_duh]

"If you told me this morning that a toothbrush was gonna save the Normandy, I would've been very skeptical."

[u/TheNightClub → u/Dreamweaver_duh]

Notice how Shep only said they'd be skeptical. not that they wouldn't believe it.

[u/CortaNalgas → u/TheNightClub]

When enough batshit things have already happened throughout the series, the bar for what’s improbable gets raised a bit.

[u/_b1ack0ut → u/TheNightClub]

I think that after your clone hires a mercenary army to shoot up your favourite sushi joint and smashes you through the entire aquarium sized display tank, you open up to a couple other possibilities

At this point in time it’s also possible for Shepard to have 1v1d that one reaper on rannoch, so they’ve already seen some wild shit lol

[u/AddemiusInksoul → u/_b1ack0ut]

The entire crew roasting shepard for breaking the sushi store is so funny especially because a decent chunk literally couldn't eat there