I don't think it's a bug. I think it's a planned effect. It mostly happens in settlements that didn't belong to you at game start, so I think it's a replacement for the culture penalty from RTW. They really toned down the public order penalties in this game. The 50% culture penalty is gone, squalor penalty to public order caps at 80% now, distance to capitol penalty has been reduced, so it's a lot easier to keep a large city under control in this game. I expect the permanent unrest (if that's what it is) was put in the game to give you SOME little difficulty to overcome keeping acquired regions under control. I just haven't been able to find it in the files where it's controlled.
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