Certain factions will attack me despite my reputation with them. I'd like to start by saying I am well aware that wearing certain faction armor as well as having certain companions in your party will turn other factions hostile towards you.
It started with the Wild Card: Side Bets quest when I was first trying to make contact with the Brotherhood of Steel. I would walk into their bunker and before even getting to the intercom they would run through the door and slaughter me. I tried wearing no armor, dismissing my companions, going during the night instead of day, but they still kill me me. I fixed this by recruiting Veronica and traveling with her to the bunker.
After finishing with the BoS I decided to go to Red Rock Canyon to meet the Great Khans. Since I was idolized with them from helping them in Boulder City I figured I wouldn't have any trouble. I made my way to the canyon and everyone was friendly to me. Until I walked into the building to talk to Papa Khan, as soon as I entered the building everyone in there immediately turns hostile. Once again I loaded a save and tried dismissing my companions (Cass and ED-E) as well as removing all my armor but I had no luck. Eventually I just decided to wipe them all out.
Now I'm at the part right after confronting Benny at the Tops. I left the tops and received the Mark Of Caesar. I talked to House and have the quest Render Unto Caesar as well as The House always wins (Part 2 I believe) I went to get on the boat to Talk to Caesar but the Legionary that approaches me to ask what my business is turns hostile towards me right after I show him the mark or use the speech option to tell him I'm a trader despite him saying its okay for me to pass. I tried putting on Legions armor and it got me into the camp but if I take it off or go near a guard dog I get attacked. So I tried leveling up twice and wasting 30 skill points getting my survival high enough to get animal friend in hopes that the dogs wouldn't attack me, they don't attack me but the guards near them still do. I even managed to use a stealth boy to sneak past the two in Caesar's tent and talk to him and receive the Platinum chip but as soon as the conversation ends everyone in the tent gang bangs me with powerfists.
On top of it all now my game will freeze whenever Cass kills someone. I haven't tried swapping her out for another companion, only dismissing her, so I'm not sure if its exclusive to her yet, and I'm too frustrated to test it. I've checked the disc and it has no scratches on it at all. Anyone having similar problems? Any way to fix it or do I just have to start the game over?

Apart from the bit at the end about Cass, I am having all three of the same problems in the exact same way!

The Brotherhood were hostile even though I had never had any encounters with them; I couldn't use the password. Resolved only by taking Veronica which I was not wanting to do; I knew the passcode!!

The Legion at Cottonwood Cove are hostile the minute I finish a conversation. Yes I do have poor rep with them, but then why let me show him the Mark of Caesar (achieved by wearing Legion armor) proving I was invited and still kill me?!

The same at Red Rock with The Great Khans. They are not generally hostile towards my, all except Jerry the Punk (there's a mission I can't do because he shoots on sight, note I have a great rep with the FotA so it's not that) and everyone in the house! I even did the drug side quest and got my rep with the Khans up to "Accepted" and then "Liked"; they still shoot me if I go in the house or approach Jerry the Punk.

It's a clear bug in the game development that is getting reputation mixed up or sees poor reputation where it should be neutral or even Liked with some factions. I want to talk the Khans out of siding with Caesar, I wanted to approach the BoS and do the little sub-quest to get them to trust me (with the collar, by-passed if you take Veronica, despite having the code to supposedly get in), I wanted to speak civilily with Caesar after I was invited to go see him at the fort and had the Mark. The game contradicts itself!! Frustrating.

I have looked these issues up before and a lot of people have the problems when they have high rep with other factions such as the NCR, but when you also have high rep with the faction in question (ie: Khans) this shouldn't matter! It seems like the more you play the game the more you are penilised!!