I found a skeleton in a desert biome who wasn't burning in the sunlight, and tried to kill it with my sword. My first hit (critical) caused no knockback, and thereafter I couldn't hit it. It makes the same noise as invisible ArmorStand or FallingSand entities when hit. I realized it was facing due south, and does not take suffocation damage or fall. It pushes back the player like a normal entity would, but is not pushed in turn. It is perfectly centered on top of the block (-209, 65, 390).

Steps to reproduce:
Unfortunately, random chance. Likely a bug with spawning though, so you could try simulating natural spawns above a void until one of them floats, then check all your variables and such. This is just speculation though, and, as a fellow programmer, I realize how annoying random chance bugs can be to fix. "Why couldn't it have just crashed?"