Human primal instincts are very interesting. For example, (most probably) every human has a negativity bias, which was developed in order to protect themselves from danger. If you heard a bush shake in the forest, fear would be the first thing to come to mind. This is, of course, rational because you do not know if there is something dangerous in that bush, and moving past it or away from it would do not harm. Maybe the uncanny valley feeling comes from interactions between past species. Maybe it came from our familiarity for each other and fear for the unknown. Maybe the negativity bias ingrained in our brains causes us to suspect something is off, causing that uneasy sensation.
These kinds of questions make me think of the bicameral mind. There is a theory that states that, in the past, humans heard a voice in their head that controlled them. I don't know much about the theory so that might be vastly incorrect, but it is very interesting to think about.