Spoiler
and they are just starting to respawn plus I don't want that big of a bounty right now.Forsworn Conspiracy
The only things I've done since leaving were kill some bandits, kill some forsworn, kill some animals... Didn't even kill any Thalmor agents.
I also discovered Sky Haven Temple by mistake. I couldn't do anything once there, so I left. I think that could be it, I've never made it that far into the MQ and I don't know if killing all the Thalmor happens before going in there. If so this could be a glitch because I went there, and I assume if this is the case it is permanent. If so, will this mess up any future quests? I know there is something about their embassy, is killing everyone from the start(because they are hostile) an option? I just want to make sure this isn't a long term problem before I play another hundred hours. I would rather load an old save now to fix it.
I also killed some Vigilants of Stendarr before entering Markarth. I know I've seen issues before where I kill someone... no witnesses, but then half a mile down the road someone else is hostile because of it. For instance killing a farmer, then the next random spawn point was the Nobel with a guard. Guard tried to attack me, and when I killed him it gave me a 1000 bounty so of course I had to kill the nobel and his horse so there were no witnesses. But I think if this was the issue the guards would have attacked me long before the Thalmor..