[minor early-game spoilers]

OK, early on in the game I helped the Powder Gangers in prison with their missions, a bit. I was more friendly with the NCR, though, and when the gang learned that the NCR was coming to the prison I ran for the hills to let them all sort it out.

Many hours and levels later I am an NCR hero and return with Boone to the prison to find the NCR shooting it out with the remaining Powder Gangers. As soon as I walk in on the firefight, the NCR are all hostile to me and immediately engage me. Self-preservation kicks in and I clear the place of every living thing (save myself and Boone). After the firefight, Boone stops me and lays this guilt trip on my about how the NCR "isn't perfect" but he doesn't want to kill any more of them. I thought to myself: "didn't I see you run in there and start shooting them?"

I figure I must have done something wrong, so I reload my auto-save upon entering the room I decide to stay out of the fight and see how it resolves itself. No luck, as soon as Boone spawns next to me he rushes into the next room and starts shooting. I figure I can't stop him now, so I wait to see what happens. Sure enough, he kills everyone in the place and then comes to me with the same sob story about killing NCR!

What is the deal, here?

#1) why do these particular NCR attack me on sight when the rest all love me?
#2) why does Boone rush in an attack his friends?

Here is my theory...

1) It must be something with the scripting in the event and these particular NCR see you as an ally of the powder gangers and thus see you as a threat..
2) Obviously, if an enemy starts to attack at you then your companions are going to respond by attacking them...

I'm having a similar problem with the NCR. I did the quest to get Boone then decided to do the Mojave outpost quest where you clear the road. I kill all the ants and fast travel to the outpost, when I get there all the troopers started attacking me. I reload to before I cleared the road and look at my reputation page, NCR isn't on the list and I could have sworn I was neutral with them (the world map also shows I'm neutral with the outpost. I fast travel to Helios one and the same thing happens. I fast travel to the NCRCF where I helped them take the prison and they are fine with me. I have have no idea why they would attack me.