That Still Small Voice - S1-E5
Continuity mistake: During Henry's first therapy session, as Archie says "So all the crickets in Storybrooke, they were once people too?", Archie's holding a coffee cup in his hand. In the next shot, the cup is sitting on the table. (00:02:45)
That Still Small Voice - S1-E5
Continuity mistake: After Regina tells Emma to clear the crowd away after Henry is rescued from the collapsed mine, Regina's hand goes from being on Henry's face to his side/waist between shots. (00:34:35)
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.