You didn't mention how long you've been in their lives, or how much time they're at your house.
I'll just add another perspective. As a child, I spent lots of weekends at my old aunt's house. I remember waking her up in the middle of the night to ask her if I could use the bathroom. I was very close with her, very comfortable at her house, and there were no kinds of issues like you've described. I think she probably thought I was scared of the dark, so she actually would take me to the bathroom. I wasn't scared, but at the time, I just felt like asking was the polite thing to do. Looking back now, I can see I was just being a dumb kid.
I hope these issues get taken care of sooner than later. Chances are, they probably have lots of confusion about how to please adults right now. They want everyone to be happy, and to be happy with them. They are very fortunate to have a dad and step-mom who love them so much. I hope the little guy is feeling better. Keep us updated.