Well, to be accurate it was Master Quest, but here's what happened.
I was in a room in the Dodongo Cavern where you kill 3 Dodongos and then there's a little "cut scene" of the door being opened. BUT I was in the middle of climbing a ladder when the "cut scence" started, because it takes so long for the Dodongos to actually die (they die, but then explode a couple of seconds later). So when the "cut scene" ended I was still on the ladder, but Link was displayed in the standing position, and the game was completely unresponsive to controller input. I tried turning my Wavebird on and off, and even switched to a normal controller but to no avail. I couldn't even pause and save my game either.
So BE WARNED, do not start climbing a ladder if you think a cut scene is about to occur!