Few things that don't make sense about the end of this movie (spoilers)
1. If Tiffany switched bodies with Jennifer Tilly, then that means that Jennifer Tilly should be in Tiffany's old doll body, but she doesn't appear to be in the final (birthday) scene.
2. The seed of Chucky (Glen or Glenda, whatever you want to call it) could only transfer into one body. They made that clear during the scene when they were trying to decide if it wanted to be a boy or a girl. Yet, in the final (birthday) scene, it would appear it was transferred into both babies bodies.
3. Chucky died when Glen/Glenda chopped his head off. But in the first movie, they said the only way he could be killed is by being shot in the heart. In the first movie, he was still alive even after they blew off his head, arm, and leg.
I know it's just a movie and you're not supposed to overthink it, but this type of *beep* really bothers me.