I remember reading somewhere, haven't a clue where, that they may have been caused by efforts to keep him alive on his transportation from Mustafar. I have no idea if this was a reliable source or mere speculation or what type of resusitation techniques could have caused the injuries. And if I'm not mistaken, when the mask is lowered onto his face near the end of Revenge of the Sith, the scar across his face/cheek is not there, only burns.
Does anyone have any ideas? It's just a little puzzle that's nagged at me for a while.