I think that Henry’s father did do something to Emma though i think it may be a misunderstanding. I don’t think that Emma is lying about the fact that she believes the father did something to her. She is way too angry for it to make sense that it is a lie. I have always thought that whatever happened, whatever the father did, caused Emma to go to jail, but we have no proof of that. Not that she is completely innocent in whatever caused her to go to jail. It does seem that she is complicate in some way and not that she just didn’t do it, but who knows. I just always have the two events wrapped up together because we know that Emma got pregnant went to jail and then found out she was pregnant so those events were close together in timeline. A lot of times it seems like the writers are flying by the seat of their pants so who knows how much of that they actually have planned out.