I'm playing as the Babylonians. My empire only stretches from Constantinople to Delhi - the stupid Indians declared war on me, and I had to force a surrender from them, but didn't want to raze the holy city of TWO religions (otherwise, my empire would extend no farther East than Parsa). I razed all their other cities (they never capitulated... the bastards). When the Arabs attacked, I kept Mecca and razed the rest; when the Egyptians declared war on me, I took two of their cities and let the rest go Independent. I never took Athens, either (ironically, the Greeks HAD declared war on me, but I was busy with the Persians and missed my window; Romans beat me to it and I wasn't in the mood for an unnecessary war of aggression. Besides, I had no exit strategy, and Athens had no WMDs).
Anyway, despite my relatively small number of cities, my empire nonetheless gets a wee bit unstable and goes into civil war. Whatever, right? I can take those cities back. In fact, I might as well let Delhi go free since it's so far away. So I go to the huge f**king army that I had stationed in Babylon (in preparation for the impending Ottoman onslaught), only to discover that my Babylon itself - my capital city! - had declared independence from the rest of the empire, and Hattusa was my new capital. Like... dude, WTF? How can the seat of government declare independence? That would be like if President Lincoln and Congress agreed to join the Confederacy and make Washington its capital, and the Union moved its seat of government to San Francisco. It just doesn't make any damn sense.
Anyway, I had basically no chance of ever getting the city back. It had all of my Wonders, so I couldn't count on culture-flipping it, and it had all of my surplus troops, so I couldn't take it back by force.
This scenario should be modified so that the capital city can never secede during a civil war.
Also, note to self: consider razing cities more often.