We Are Both - S2-E2
Revealing mistake: When Regina is trying to escape on horseback, as she says "Come on, Rocinante, go!", you can see that the one who's actually riding the horse is Lana Parrilla's stunt double. The stunt double's face can also be glimpsed when Regina is caught by the tree branches, and when she drops to the ground. (00:05:20)
We Are Both - S2-E2
Revealing mistake: When Mary Margaret tries to escape and Mulan uses a sling to bring her down, you can see that the one who falls to the ground is Ginnifer Goodwin's stunt double. (00:39:50)
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.