I think the only one I accidentally triggered was getting stuck in Verminator's room, and that wasn't a big deal. As I recall, you could just reset and replay that part properly. (For some reason, the first time I played, maybe I got lost, I entered Ebon Keep then walked all the way back through the secret path to the chessboard. Entered Ebon through the back, tried to leave and got stuck. I don't know if your game would be corrupted if you saved talking to the queen before defeating Verminator, but as I recall the only save point was to walk back through the secret path a third time, which sounds unlikely.)
Losing the Windwalker was much more serious, but pretty unlikely someone would accidentally do it.
I think the other accidental one was loading a save that was made while a status-boosting spell was in effect would corrupt your stats. (it would load your normal stats, and then when the spell wears off, it would reduce and possibly underflow your stats. So you could get like 65K defense power. :P )
I recall Secret of Mana also had glitches related to saves made while stat/elemental boosts were in effect.