On Pc.

Not sure how to explain it but my game save is either bugged or theres something going on I can't see. My companion Rose of Sharon Cassidy keeps pointing her gun at me and taunting me but she never fires a weapon or anything. Ed-E occasionally does the battle song as if theres an enemy nearby. Any where I go npc s all around act as if there is a gun fight or danger nearby but nothing shows up.

So I'll let you know what I think triggered this and its possible fixes.
I was doing the Beyond the Beef quest where I have to investigate and find Heck Gunderson's son. Well I reached a point where I'm supposed to find an investigator inside of a room. I was given a key to the room but heres the thing I don't remember, I do not remember if this door was signaled red or orange. Needless to say I found the investigator in a less then perfect health condition. After which two guards start attacking me and Sharon Cassidy. I didn't have any hidden weapons with me and I seemed to lose a lot of stimpacks keeping Sharon alive so I Made a run for it and spawned us outside the casino.
This is where it starts happening. Everyone acts like theres danger near by, possibly because I didn't kill my attackers. If I enter the casino they'll start attacking me. However, if I kill one of the two guards who were attacking me everyone starts attacking me which isn't what I wanted.

How do I eliminate these two threats without alerting everyone else to me? I think this is why my companions are acting as if they are in combat all the time. I tried sleeping it off, reloading. Everything. I know I have to eliminate those threats. But I dont want to ruin the entire casino.

bump

Since you're on pc you may be able to use the console to reset that quest. Since i'm not a pc user i'm not 100% sure

You have to kill those two White Gloves inside the room where you find the investigator's body; if the fight spills out of the room, all the White Gloves will turn hostile. And they're tough enemies.

If you have a save prior to entering that room (and you should save frequently during that entire quest anyway - it's buggier than a radroach convention), one thing you could try is to fire Cass and pick up Veronica as a follower. She's much better at unarmed combat than Cass, and if you give her some decent armor she can handle those White Gloves pretty easily with just her fists. Also, if you can buff your Sneak skill up to 50, you can carry holdout weapons for you and your companion past Ultra Luxe security, and that'll make the fight much easier as well.

just use the setally console command...

I am fairly sure that the reason this happens sometimes is when they follow you down steep slopes, they think they've taken damage falling so go into combat mode but can't find any foes. Same happened with companions in FO3 for me. Usually saving and reloading sorts it out, or engaging them in conversation.

Edit to add: sorry I completely failed to register when in the game this was happening for you, no steep slopes there. Try a save and reload anyway.