The only thing I did was kill two rangers for their ranger armor (For me and Boone) but I did this by placing a c-4 and detonating them from a safe location, so this should not have done anything. The only other thing I can think of would be me wearing my Ranger Armor and it saying I was dressed like the NCR... But still I don't get it, what happened?
*Update* Just noticed my Powder Ganger, Caesars Legion, and BOS rep is neutral as well when the former were both vilified and the latter Idolized. This better not affect the pact I made between the NCR and BOS