When you get a mission to kill x number of ships from an AI, destroying buildings counts towards the mission targets.
In the included save, I have a mission to destroy Red's ships. The current count in the save game is at 9 ships left to destroy. I have a fleet attacking one of Red's planets - just destroy the lab on it and you'll see the counter drop to 8. No ships anywhere nearby.
http://rapidshare.com/files/155370733/ShipKillBug.save.html
