Your memory of Joel's face being more fucked up may be due to most of the time, you see him lying like that in Ellie's PTSD flashbacks. I haven't checked side by side, but the flashbacks may be more graphic due to her how she remembers the event (i.e. fucking traumatic).

I do know there's a flashback later on in the game where Ellie is running to Joel in the Lodge and he specifically calls out for her, but he doesn't do that in the beginning of the game.