This involves just Custom Factions and Sovereigns. Some times when going in the game all the Custom Sovereigns are headless. And this happens on every picture you see of them in the game. Saving game then logging out and back in still have same issue. It is funny because if I equip them with helms you can sse the helm on top of an invisible head.
However this does not happen all then time but once it does for that particular game they will be headless for the entire game.