As I explore my world in survival, I find random skeletons that do not respond to the player. They do not shoot, turn towards you, move, or burn in daylight. You can walk right through them and it does not respond. It also takes no damage when hit, and arrows go right through it. This happens in all difficulties, including peaceful.

I also had this problem on a larger scale with a naturally placed skeleton spawner. The room was completely filled with skeletons, all like the ones I described above, some were even sticking out of the floor and ceiling. The ones on top of the chests prevented them from opening. When I refreshed the world, it all happened again.