Revealing mistake: When Hook is running from the Lost Boys, as he clambers down a hill, you can see the face of Colin O'Donoghue's stunt double. (00:00:50)
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)
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.