Continuity mistake: The way the baby blanket is wrapped around the infant Emma repeatedly changes between shots. For example, as Charming approaches the magical wardrobe, the blanket has just a tiny opening over the baby's face, and the embroidery with Emma's name on it is showing; in the next shot, the opening is much bigger, and the embroidery can no longer be seen. (00:30:00)
Continuity mistake: When Henry is in Emma's apartment, the amount of juice in the bottle repeatedly goes up and down between shots. (00:08:40)
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.