True North - S1-E9
Continuity mistake: As Emma returns to the apartment, Mary Margaret is folding clothes on her bed. As she sees Emma, she's holding out her arms, but in the next shot, her arms are down by her side. (00:37:05)
True North - S1-E9
Continuity mistake: When Hansel and Gretel are outside the gingerbread house, Hansel dips his finger in some icing on the wall, which leaves a mark. Two shots later, more of the icing is missing, even though no one touched it. When Gretel climbs onto the window sill, the icing is fully coated. (00:17:50)
True North - S1-E9
Continuity mistake: When Emma and Mary Margaret are conversing on the bed, Emma's sweater moves up/down her left shoulder several times. For example, as Emma says "Apparently that book you gave him, aren't exactly the stories in the most traditional sense", the sweater is over her shoulder. In the next shot, it's off her shoulder. In the following shot, it's covering her shoulder again. (00:37:45)
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.