Pretty hilarious but non-breaking bug:
Playing with revolutions, on a pretty big water map, so lots of colonies/rebellions/etc... Apparently the "get new leader" script ran out of leader options, so when Julius Caesar decided to make a colony of Japan, the leader was "Barbarian" with Sid Meier's head. He promptly demanded I give him some technology.
Now he's demanding I convert to Confucianism! What a mean dude.
Oh, another minor one:
Playing as Sioux, and the carrier unit graphics are messed up. It shows the "damaged" state (with holes in the deck) even when it just came off the shipyard. Haven't had a damaged one to see if the damaged state is using the undamaged one (i.e. they were just swapped).