And Emma is clearly very emotional at the moment. I think it makes total sense that when your emotions get in the way it is harder to tell because you are not being detached and just watching them. Snow is unconscious and Emma is annoyed, it isn’t like this is an easy situation.
I think it is just that Emma is really good at spotting a liar and it isn’t as if Cora is lying, she is just being creepy, but that is also because we know what she has done. Emma is not used to a world where people are as insane as Cora or Regina or Rumpel.