I blew up a few doors with bombs and bombs+, with a lot of bosses guarding them, so it might be too late to use them now. I think it was in underwater vaults. Some of them bore traces of human life, called the Ancients, or something like that. Does that ring a bell?
Same here. I've restarted several times from my saves because I was missing something, but the problem seems to keep recurring. Each time, I discover a new element I hadn't noticed before. There are so many clues when talking to everyone that it's sometimes impossible to remember them all. Had I known, I would have taken notes, a sort of leger to remember where, when, and who I was talking to. The worst part is that when I see these clues (the orange phrases), I know they indicate something important, but since I haven't reached the exact moment it happens, I have absolutely no idea what to do with it; well at least most of the time.