Well, you probably won't see smoke puffs firing thru the windows as the bullet hits a wall somewhere 15-40 feet inside the building as oppossed to hitting above and below it outside.
Since the windows just aren't there; just air (you can check it in the SDK), there shouldn't be any problem with a window blocking a shot. I myself killed two players in the windows with a bolt from somewhere in the center of the commons; a far shot. I did miss quite a few times too (I was a Russian shooting Germans...)
I can only suggest lag or player movement at this point?