I don’t think it has anything to do with magic. There are some people who are really good at sensing if others are lying or not. Seeing as Emma always did this, I don’t remember what it was called, bail-something job and has been searching for her parents, thus acquirering all these detective skills, I think she’s just very perceptive. But I don’t think she can always tell when someone’s lying, since she doesn’t seem to have picked up, that Sidney isn’t on her side (I guess we'll see something about that in the next episode.).