I was doing Cass's companion quest, and I had to kill that lady in the Crimson Caravan. I didn't want to gain NCR infamy, so I put on a legion disguise before taking her out, but when I took the disguise off and checked my reputation, my infamy went up anyway.

Did I do something wrong?

Any changes made to your rep while wearing a disguise are applied when you take it off.

If you were going to take her out, you needed to use a silenced weapon if you did not want to lose any reputation with the NCR.
My game, however is glitched. I was Idolized by the NCR wearing nothing but T-51b Power Armor, (Not the BoS faction related one,) and after I visited the fort, every NCR soldier turned hostile against me at every camp.

I am forced to use silenced weapons to take them out so I won't lose any further reputation.

Reputation is bugged. My most recent relation related bug (there were many) is that while I am "smiling troublemaker" with Powder Gangers, some of them are hostile toward me. Not whole faction, just some in specific locations (two camps around prison). Makes no sense at all.

Jeez some men will do anything for a pretty face.

Some Powder Gangers are always hostile. I don't believe that's a bug. It's because they aren't exactly unified, and there are splinter groups who don't obey the main group (i.e. Eddie's men in the prison).

Unless you are referring to bandits in Primm who are technically not powder gangers than in my previous games no powder gangers were hostile to me once I got reasonable relation with them. They were sending however hit squad after me South of Primm. Which I assume was another bug.

Reputation ain't bugged, just sometimes finishing quest while not [Hidden] will give you infame anyways.

As for using disguise to prevent infame gain: since named NPC can see through disguise (yet they still attack you despite you would have been friendly otherwise), it just doesn't work on them......

Killing the Caravan boss is tricky...

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Also, I don't even bother with disguises. I just go in guns blazing into hostile situations, or I'll sneak if it's really important to stay hidden, and use a stealthboy once in a while.

Lot of people were experiencing various bugs. Like been attacked by faction when you are idolized. Or relations disappear altogether like you newer encountered that faction. And others. I did experience several bugs related to relations. Relations are bugged.

The only reputation bug is if your faction armor is removed due to being used for repairs the disguise isn't properly removed. The disguise isn't designed to let you avoid reputation changes.

reputation didn't bother me much as the ncr were already loving me anyways so i blew her head off with a shotgun.

I've got a similar issue. I am in the good graces with the NCR but the NCR Rangers attack me on sight. All other NCR's are friendly towards me. Then I see the red blip on my radar and it's a Ranger. It is making it very difficult to do NCR quests as there is usually a Ranger floating around nearby. I am up to a Level 22 and I hate to have to start over just to remedy this. I do think early in the game I was not in the NCR good graces. They had the roaming Ranger come up to me and said I had three days to make nice with NCR or else. Well I didn't make nice in time and the Rangers attacked me so I had to waste them. I am sure that's what this all goes back to. But I have been unable to find a way to make up for it with the Rangers specifically.

Do a sneak attack using the ballistic fist, if you don't one hit kill her reload the save and try again.