I've yet to have a rebellion/civil war/faction reappearance that I couldn't explain. In the last 5 or 6 campaigns I've done I can't recall having any of the above happen to me with a single explainable exception: when the Mongols invaded I got a message about a rebellion in Georgia--despite knowing it had well over 100% loyalty that turn. The rebels were Mongols as I recall--not much of a surprise... If you are having spontaneous rebellions, civil wars, and faction reappearances then you most likely are overlooking something.