That's terrible! I don't know very much about the topic, but, I do know that they will ignore or kill the runt sometimes, because of the "survival of the fittest" instinct. Maybe she just knows she can't feed that many puppies. I would call a vet and ask them, though. Or maybe find an animal behaviorist. Do you know from the previous owner(s) if she's ever done this before? Good luck, and, I'm sorry you and Samantha and her puppies are going through this.