During the quest Arizona Killers in which you side with the legion and And after i succeeded in doing so I got the quest notification to return to Caesar. So naturally i did so, and everyone started attacking me. I am not sure what happened but every time ( i have done this quest multiple times) I do this quest me karma with Caesars legion goes from accepted to neutral. Is this a major glitch? Or is somehow me doing this quest stopping me from being on friendly terms with the legion ( i don't know why this would happen considering its a quest from the legion)? Is there anything i can do or do i need to just say **** it and finish the game on my own terms.

Are you wearing NCR armor? Chances are you were wearing NCR armor when you assassinated Kimball, and if you're wearing NCR armor the Legion won't recognize you as an ally.

I was originally for the quest but i took it off after words. Even then though how would that affect my karma with the legion.

Wearing faction armor changes your reputation with different factions for as long as you wear it. Try putting the armor on and taking it off again, or wearing armor belonging to another faction and removing that.

The armor's effect sometimes stays on when you unequip it. What Talonfire said should fix it.