Other mistake: When Nica is dragging herself away from Chucky, you can see her calf muscles flexing and see her lift her legs above the floor for a second, even though her legs are supposed to be paralyzed.
Other mistake: When Chucky is telling Nica the story, his reflection in his knife is not mirrored, as it should be.
Other mistake: It makes no sense for Ian to have so much blood on his shirt after he grabs Nica and carries her down to the garage. She didn't have enough blood on her to coat his shirt.
Other mistake: This is hard to describe. When Nica finds Jill's dead body, you can see the side of her wheelchair and feet on the right side of the screen, and they've been laid over the top of the image in post-production. Their angle literally makes no sense. Her chair would have to be leaned 45 degrees to the side for the shot to be possible. Jill also wasn't close enough to the door where Nica is for the shot to be possible.
Answer: It is revealed when Ian checks the webcam that Chucky hid Alice in the closet. She was most likely there the whole third act.