I was playing Fallout NV and before I ever set my foot on NCRCF soil I had neutral reputation with Powder Gangers. I helped them out and when there was an option to kill NCR troopers on my way out, I went into "hidden" and put on NCR armor. I did not kill anyone but looted the bodies. NCR took the prison on their own.
After this I went into an auxilliary building and there were 2 Powder Gangers who somehow avoided the fate of their colleagues. I killed them without trying to be stealthy. Now when I enter the administrative building, NCR troopers are attacking me on sight. This is somewhat weird since I would think that I only helped them out clearing the place.
I got some positive NCR rep afterwards and now am "idolized" by them. Still, NCR troopers at NCRCF attack on sight.
There must be something weird about Fallout NV reputation system explaining this. What is it?