I'm experiencing an issue where if a room has a bubble enemy and you leave the room when you come back it turns into another enemy that is in the room. For example, say I have a room full of darknuts and a sword disabling bubble. If I leave then room and come back the bubble turns into a darknut.
*edit*
I have found that this is not the problem when the bubble is the first enemy. However, this then makes "make first enemy ring leader" useless in rooms with bubbles.