Ha, this is what makes sims like Civ so great. They are so complex you never know what will happen, and you can almost justify it via some analogy. E.g., "That bug is just a civil war as the government goes to war against a formal ally, and the populace rebels against the government"
In all seriousness thought the revolutions mod for Civ4 was one of the best mods in terms of core dynamics, and although this example here was a bug I can't wait until the modders do their magic to get a dynamic like that back again...