This isn't really related, but check this out. I couldn't get 100% completion in my copy of Metroid Prime, because of a non-existent missile upgrade. I forget the name of the level, there's a huge icecicle that you have to break to get to a grappling point in the middle of the room, then launch across and get the missile. The grapple point didn't ever appear, but I figured out another way to get to the missiles - but the missiles also were not there, even though I could scan where they should be and the game told me it was a missile upgrade. Wierd, huh?