Can't figure out why some NCR characters keep attacking me...I've checked that I'm not wearing faction armor, even going so far as to remove ALL apparel but it doesn't help. Sometimes when I defend myself all their buddies join in, but other times I kill them and nothing happens. And so far it's always been characters with names (not 'NPC Trooper' but 'Private Kowalski' or something...)

EDIT: It appears that for SOME NPC's you HAVE to wear NCR armor to speak to them...which seems stupid...'Private Kowalski' is just standing in the middle of Boulder City and as soon as I take off the NCR armor he becomes hostile...but earlier I tried to talk to a Lieutenant outside Helios One wearing NCR armor and she just attacked me, but when I killed her I didn't lose any rep with NCR or gain bad karma and none of her NCR troopers attacked me...can't figure this out...

I am having the same issue. Here is my description copy/pasted from another forum. Spoilers if you haven't figured that out from the topic title.

I have never attacked the NCR. I completed the "clear the road" mission for them at Mojave Outpost. I helped the Crimson Caravan dude in Goodsprings. I walked into Boulder and the NCR lights me up. I retried this several times, they're red as soon as I see them.

I am naked and unarmed. I even dropped all non-quest items in my inventory.

The only way past is to kill the private and take his NCR getup, then the guy guarding the gate where the Khans have the NCR dudes hostage treats me like I am me (and not a member of the NCR).

I get attacked again (regardless of what clothing I'm wearing) as I walk between Vegas and Boulder, by Crimson Caravan people.

Once I get to the NCR embassy, although I walked past all the MPs outside, the ones inside automatically attack me. Again, I am naked and unarmed. I can run up to the ambassador and talk to him, he absolves me of my supposed crimes against the NCR and tells me to talk to the Boomers, as soon as we're done talking he attacks me.

Pip-Boy says I'm neutral with the NCR. I also get attacked by the Crimson Caravan people even though the guy I saved gives me 150 caps and thanks me again.

This is annoyingly frustrating, to say the least.

K, something else that may or may not be related...in the General tab of Stats, under reputation, I see rep for Goodsprings and Novac, but nothing for NCR, Legion, or Powder Gang, or any other gang. And i KNOW that NCR likes me and that Legion and Powder Gang both vilify me...along with a couple other gangs I've come across...so what's the deal with them not showing up?

I am not as far in the game as you, but I have the same problem with my reputation screen. I know the Powder Gang shuns me, but they have disappeared from the list. They were there before.

And now the latest...I'm no win Camp McCarran dressed as an NCR trooper just in case...I've talked with several people in the main courtyard area with no issues...I go into the hangar talk to some some colonel, turn around and then there's some random trooper shooting at me. I killed him and went to "Shunned" by NCR and that DOES show up. If I take off the NCR armor he still tries to kill me but now the Colonel I just talked to is ALSO hostile...

EDIT: Dropped my companion thinking maybe he was the problem...he wasn't. This time only 1 regular soldier attacked me and when I killed him I didn't lose rep with NCR. But then I went looking for Captain Curtis...found him...and then killed him when he attacked me. This didn't lower my rep either but did make me fail one of my quests (the one where I needed to talk to him).

New update. Since that Captain Curtis was in a closed room I stood outside the door and tried a few things to see if I could get him friendly again. First I took of all apparel...did nothing except make about half the people on my radar turn red. Put the NCR armor back on and it was only Curtis who was red again. Then I put on Legion armor and, oddly, about the same number of NPC's went red as did when I was wearing no armor. Then I put the NCR armor back on and Curtis was friendly...weird...

EDIT: Did as many NCR missions as I could find, and as soon as I made it up to "liked" the Powder Ganger's, Caesar's Legion, and Great Khans all showed up as vilified...I also haven't run into any NCR troopers who wanted to kill me after making it to "Accepted" even though I'm wearing non-faction Combat Armor around... Still not sure what cause the issue in the first place but it seems to be resolved now. I'll keep updating if it reappears.

could be that you worn the Legion armor at some point? Same thing happened to me, but I just wear NCR armor walking around, and that way I don't get shot at by every NCR trooper and random merchants.