Revealing mistake: After Ariel stabs The Evil Queen in the neck with a fork, Ariel and Snow White jump into the ocean to swim away. In the underwater shot, you can see that the ones swimming through the water are not Ginnifer Goodwin and JoAnna Garcia Swisher, but their stunt doubles. (00:29:20)
Going Home - S3-E11
Revealing mistake: In the convent, when the Shadow knocks Hook off his feet, sending him sprawling onto the ground, the one who actually falls down is Colin O'Donoghue's stunt double. (00:11:10)
Revealing mistake: When David is letting Henry drive his truck, there is a close-up of Henry, followed by a wide-shot of the car where the tires are screeching, and you can see that the one who is actually driving is Jared Gilmore's stunt double. (00:30:15)
Snow Drifts - S3-E21
Revealing mistake: When future Hook is trying to stay hidden while Emma is making out with past Hook, there is a wide shot where future Hook sneaks past a corner, and you can see the face of Colin O'Donoghue's body double. (00:33:20)
There's No Place Like Home - S3-E22
Revealing mistake: After Snow White hugs Red Riding Hood goodbye, there is a wide shot where Snow walks toward Charming. If you look at her face, it it not Ginnifer Goodwin, but a body double. The body double's face can also be seen in the wide shot where Snow walks away. (00:19:20)
Answer: He knows who she is because he knows that the fairy tales are true. He was also shown to sneak out to go see Emma or someone else. Sometimes he succeeded, sometimes he didn't. This is how he knew to look for her despite his strict mother.