1. Right click the floor of a classroom to remove it.
2. Try to remove the classrooms and then designate them again.
I am really interested in the idea behind this game. But it needs some determination and dedication from the devs to turn this idea into reality.
There is not a lot of content, but I understand this is still in the 'Pre-Alpha' phase. The devs are probably working hard on the next release, so it hopefully should come out soon.