Only about 15 hours into the game, haven't reached The Strip, and I haven't been using any faction armor (only the reinforced leather and the radiation suit). I noticed this bug happening right when I started the Nelson quest. I killed the Legion outside and set the NCR prisoners free, but when I went inside one of the barracks the Legion inside was completely neutral and acted as if I didn't slaughter all their men outside. Just to verify that this was the case, I traveled to Cottonwood Cove. In the past I know that the Legion here would attack me on sight, but now they are completely neutral.

My pipboy states that all my faction relations are correct and that I am "vilified" with the Legion. I am also vilified by the Powder Gangers and I checked to see if they were bugged and I went to the NCR correctional facility only to get shot at by the Powder Gangers. I tried resetting the faction reputation via the console command but that hasn't changed anything. Can anyone give me clues as to why this happened and how I can fix it?