Having watched mobs a lot, this bug is generated when the mob uses stairs, or jumps up one block. It seems to be related to how high the mob is jumping. Hope this helps. I can recreate this bug with any entity in the game, so it is systemic, not conditional.
Yes, this is confirmed for 13w42b, just got killed by a baby pigman, and all I could see was his sword and the top of his head sticking out of the ground.
I get this too.... AERO is basically "transparent tabs" and a totally useless feature of windows. Disabling it solves a grocery list of problems with too many games to name.