Did you get the patch? I remember those and I believe I fixed them.
Just got the patch, however haven't touched it yet.
I almost wonder if it's a bad thing having all the building's interriors accessible. As you mentioned, there's arrows everywhere
BTW, interesting and nice touch with the assassin underground tunnel (The large skeleton which you can't see). I accidentally went through the floor and noticed it. I think it's cute and original. Course in game you normally don't see it or know what it is.
EDIT: Also just remembering. For some reason my unarmed and mysticism skills are damaged. What creatures would do that, and where/how do you cure yourself? In all the games so far i don't know of anything that damaged skills, so there was never a restoring for skills either.