Hmm... I'll have to take a look at the sky height, I thought it was high enough.
Am I using the grid? Sorry but that made me laugh. Yes I'm using the grid. Sometimes a 1 pixel gap will save a few numberportals by not breaking up the surface. I'm not sure if it saves anything in this case but I believe you're talking about crates in the hallway with the pipes coming out of the floor. If so it was done on purpose. If that's not what you're talking about then you'll have to be more specific.
Thanks for looking at the map, if you see anything else let me know.