I've looked at multiple blogs and I think I'm the only one who noticed this. Pay close attention to Kate as the show jumps around to different years. Notice Kate before the abduction and after. Look at her hair part. One Kate has her part almost directly in the center of her head. While the other Kate has her part above the outside of her left eye. It's two different people. Twins with their hair parted in different locations on their head playing two different Kate's. A person can't change where their hair is parted. It's growing out of their head!
In some episodes, they will show the top of Kate 1's head and immediately show the top of Kate 2's head in the next scene. They are trying to show us it's not the same person. The Kate who disappeared is not the Kate that came back.