I have an idea.
I've seen that when I keep on conquering regions and/or winning battles I see a public order boost called Triumph in many settlements. So to take care that this Unrest won't bother you too much just keep on conquering :P lol.

But seriously, I have this problem too, yeah. I was just thinking "Hmm, what the heck? Is it just because of spies?" Then I thought it could have to do with religious unrest and others that create a global unrest or something? Or maybe spies have been to my settlements and then left but the unrest stayed?

Well, whatever it is, I don't like it.