I've had a bit of a think about point #2. This only seems to happen with objects that use overlaid sprites (Fire Man's body is a separate entity from his face. I also see it on all the other robot masters except Cutman, who does not have a separate face entity).
So that may help guide investigation a bit. I'm not sure if this is a 3DNes flaw, or some inextricable detail about NES sprite display.