There are three hidden trophies. Which two do you already have that aren't named on this list?
http://www.oddworld.com/2012/07/munc...d-trophy-list/
The bad Quarma trophy should have unlocked. I've not heard of it being bugged. Is there any more information you can give, like how you started the game, or what the latest save is before you reach the end of the game?