Fallout 3 as well as Oblivion has a few "location" bugs in which generally the devs mixed up two or three entrances to an area. Sometimes you enter a building (or cave, in Oblivion) through the left door, but when the inside area is loaded, you are at the right door. It's confusing sometimes, but since they're not major experience killers I never paid much attention. Never came across that building you say (with the bottom door leading to the roof), though. Where is it?
As for the rifle, have you tried VATS? It shoots in your behalf