How was the puppeteer able to convince the police so well about his story? Examining the Diploma on night 5 reveals it is for acting, so naturally the man would be pretty good at controlling his emotions.
Why is the Puppet the one talking to you in the beginning and blaming Mary for the deaths? Because it was his fault, and if he convinces Mary it was hers, she won't be able to remember!
If Mary's little brother is actually Mike Schmidt, then think about this: he was already attacked by one haunted animatronic. Now, he's getting attacked by five! Poor bastard...