If the surface the hole is on is not flat or perpendicular to the view, then it may not be a circle.
Well, the box does have a draft. I cut the big holes right on the drafted face, and but smaller holes I sketched on a plane because the parts that went in them looked funny. I'll have to sketch the bigger holes on planes too.
EDIT: I just moved the sketches to a plane. Now I have center marks, but my hole isn't very pretty anymore. Oh well. Job done!