>>12183742>>12183807>>12184407No. It comes from the brain recognizing it as a face, but failing to resolve its features.
Similar to how you may perceive languages, or certain language sounds, as ugly. Such as the velar fricative - it's a very distict sound, yet the brain has no category to place it into, so it will (for an English speaker) analyze it as "a very wrong h". This "wrongness" is what causes the unpleasant experience: the brain knows its analysis is incorrect, yet it has no way to analyze it any better.
This applies to most uncanny, creepy, or otherwise inexplicably unpkeasant perceptions.