It's been a low-level issue my whole run. I sneak, pickpocket or steal and succeed on all my checks, but a guard still shows up suspicious of me. So far I've been able to ignore it.

But just now I was in Grymforge and talking to Elder Brithvar and Stone Guard Kur, and they asked me to destroy the scrying eye orb. Well, after the conversation I notice that the eye is right next to me, and there's no other NPCs nearby besides the one that just asked me to kill it. So I attack it and kill it, and immediately Stone Guard Kur accuses me of a crime and I have to pass a Deception check to get out of it. She was just part of a conversation asking me to kill it!