Do you recall anything unusual happening at that time? Did you attempt to do something in the newly unlocked room? Did you issue an order to the crystal bot to follow you? Were you doing anything unusual such as moving the crystal bot to the end of the level, while there was already a wave in progress?

No, I played it again, and the game legitimately freezes at the final door for a second or two while leaving the Crystal Bot wide open.  During this time it can be destroyed even though the stage is over.  I guess it doesn't really matter though because the game promptly crashes immediately after that during the loading screen.