I have one box that is not square. The bees will use the gap as an upper entrance, if I put the box on the right way. Otherwise, I think they fill in the hole.
I'm pretty sure the foundation I set the hive on is not as level as it was at first. The bees, being more of a perfectionist than I am, have built their comb perpendicular to the ground, rather than to the walls of the hive. As a result, those foundationless frames I put in the box have resulted in a box of comb that blends from one frame to the next. I've given up pulling all of the frames out to inspect that box. I'm waiting on the nectar flow to hit, then I'll just pull the whole box and see what I can do.
For now, the girls and I have agreed to disagree on what the comb is supposed to look like.