I had an issue so I reverted to a previous save nowhere near what I wanted to do.

I had a white glove disguise on and when I looked after a killed benny in normal gear, I had a neutral rep with the NCR and Caesar's legion, heck, every major faction in the game was neutralized.

I just need to know what NOT to do in the future so I can try to get the reputation levels up to get ALL the safe houses.