Continuity mistake: When Henry is sitting at the bar at the end of the episode, reading his storybook, in some shots, there is a picture on one page, which takes up the entire page. In other shots, there is a different picture there, which takes up only half the page and has text next to it. (00:37:25)
Continuity mistake: When Gideon shows his father the book that Belle gave him, "Her Handsome Hero", in the close-up, the cover of the book is facing upward. In the next shot, where Mr. Gold takes the book, the cover is facing downward.
Continuity mistake: When Emma lands and Hook land in the apartment after going through the portal, Henry and Regina help them both to their feet. In the first shot, Regina is seen holding onto Hook's arm as he and Emma get up. In the next shot, she is holding onto Emma's arm. (00:34:45)
Continuity mistake: When Mary Margaret drops by Emma's house to discuss wedding plans, in the wide shot where Emma's phone rings, Emma's flower tattoo (which can be seen in several other shots throughout the scene) is missing from her wrist. (00:04:15)
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.