...As soon as I start a battle, my troops shoot out all the doors in my fort, often killing each other in the process? This is pretty frustrating. Can it be fixed, or is it just a problem with AI to be patched up in later builds?

Err, that would be because the doors are set as the enemies, and uhh... Crap. I forget how to fix it. :F

You pretty much have to manually fix the map. Editing the .ini et cetera.