I was wandering around whiterun at about level 9 when i ran into what i thought was bandits walking up a hillside. When they attacked, i realized they were thalmor in elven armor. I managed to kill all 3 and to my surprise i found a execution order on one of them ordering my death, but i never saw any of these guys before... Have i done something in another way to have them hate me? At level 9 all i did so far was some companion quests and raiding bandit caves. Will this keep up?

No, my character that I have 70+ hours into seemed to run into two. One with the execution order, and another one that was wandering around killing Stormcloaks...

I've encountered 2 Thalmor execution orders, I believe it keeps happening as a random if you infiltrate the Thalmor ambassador quest.

I've killed dozens of Thalmor, both in the wild and multiple sweeps of the Embassy, but I've never gotten a hit squad after me.

I havent went to any embassies. This was my first and only time encountering them. I have no idea why theyd want me dead

Heh. The Dark Brotherhood sends assassins out after you too - even if you've never done a thing in re the DB.