The scene introducing Munn's character was cut, for understandable reasons (you can find the details online), but it was never re-shot. That's the reason why her character first appears in the theatrical cut with no explanation of who she is. Black's original ending featured the humans and "old school" predators working together to fight the "new predator" and it took place at night. The studio demanded that Black discard the ending and shoot a new one. Edward James Olmos had a role in the original ending; all of his scenes were cut. I suspect there might have been a scene explaining that Jake Busey was the son of Gary Busey's character from Predator 2 that was cut, as well.