*spoiler* Emily not telling David who Charlie really was
I feel like we needed a flashback scene during David's big revelation that showed Charlie explaining to Emily that he isn't her father and threatening her not to tell her father that they share the same body.
Without such a scene it's hard to believe that Emily wouldn't just tell David that *he* was Charlie. Especially during the scene where she gets in trouble for defacing the bathroom, and the scene where he interrogates Emily about Charlie's identity.