This theory is about the animatronics knowing that the person is a human. If they think he's an endoskeleton how come they don't attack everyone during day? Are endoskeletons only able to move at night? How can you mistake a thin metal stack of beams compared to a squishy warm human?
Animatronics are not dumb. They can walk around during the day and locate a Security Office and won't move when cameras are displayed and can disable them for a short amount of time. They can stuff a Night Guard into a suit. How come they don't stuff the endoskeleton in the Backstage (FNaF 1)
In FNaF2 there are rare occurences where an endoskeleton may appear. How come the old and withered animatronics don't attack it. In a FNaF 2 Phone call from Phone Guy he mentioned that the old animatronics still stuffed humans. This is extremely fishy!
In conclusion, I know and believe the animatronics are murderous killing machines but I also believe they know perfectly well that the Night Guards or 'endoskeletons' are humans. This is very fishy! To me it seems that this may be more than a glitch.