Indeed. I just completed the whole game, and only got TWO trophies. None of the chapter trophies unlocked, just miscellaneous ones. I really don't like the idea of having to do a whole nothing playthrough.
Edit: omfg. Looking at Pyx's guide, it seems that there are no story-related trophies, that everything unlocks based on miscellaneous tasks? Okay, so maybe it won't be so bad doing the trophy cleanup.