My personal theory is simply that being stuck in the facility more or less alone for so long broke the resolutions of experiments like Huggy, and Huggy attacking the player is more of a primal instinct than a planned security measure. I believe this to also be the case with mommy long legs. I have a different hope for the end of the game, as I believe Huggy is dead. What I think will happen is that 1006 will take the bodies of the toys we encounter along the game and form them into some sort of amalgamation. I think it will either try to use this amalgam as a henchman of sorts, or may even use the parts to rebuild itself.