Yeah, I don't know what the hell happened to do this. Clipped through a wall? Dropped into the background layer from sprite overload somehow? (All the pirates in that one room were concentrated on screen when the glitch first triggered.)
Every now and then (read: I don't know what triggers it) the area location moved to where Samus 'was' at the time. It could trigger the Pirate Alarm, though neither they nor Samus could actually shoot each other.
I did actually manage to trigger a room transition at one point, arbitrarily. Couldn't replicate it later when I went back to the savestate I put in glitched-mode.