Right to the point, I read in the latest patch notes that they have fixed something with the reputation right? I personally thought that this involved the bugs that come with reputation gaining.
I googled a bit and only found people having the same problem and no fixes that doesn't involve the console commands, the problem I have consists or gaining vilified status with either the NCR or Caesar's Legion and still being friendly too them. What is the deal? With the amount of complains I would of thought that in the latest patch they would of corrected the mistake but it seems I was mistaken.

Or I may have overlooked a fix or something so does anyone know how to correct this? Again without the console commands.
Also I was not wearing Faction armour, I've tried everything I could think off so any help would be appreciated.

Take off your faction armor it acts as a disguise, that's my best guess.

I've read some people have issues with all rep being reset to neutral after wearing ... uh... the white glove society item, I forget the name. Perhaps you ran into something like that?
Don't know of a solution for such faction bugs, beyond a possible fan-created mod-fix, if one exists.

I've experienced this, I murdered Vulpes Inculta and razed the Legion Raid Camp and killed the Legion Assassins they sent after me... Less than a minute later I walk across a Legion patrol, they are all non-hostile, but they do say "I'd rather kill you than talk to you." but don't attack until I headshot one with a Throwing Spear...

As I said I was NOT wearing Faction armor.

And Mako quite similar to me, right after Nipton as you walk up the road with the mines under cones there is a patrol of Legion, after I kill them and the assassins they go to neutral. I've tried avoiding them and killing others but same thing happens. Also with the NCR too. I thought the patch fixed everything to do with rep, urgh its getting quite annoying. I've stopped playing until a fix, I prefer being attacked.