In the mission to obtain the Pirate Mothership, you can attack the Mothership instead of coming close to it to trigger the dialog with Ternie. I blew it up expecting to get a hilarious reprimand and game over, but the game crashed instead, and LOGfile.txt containing the following:

It's not really a bug per se, it's just that the game script never assumes anyone is insane enough to destroy the ship; I suppose the crash is due to the game unable to find the ship (since you blew it up). This can likely be fixed by adding a check for destroying the ship, similar to the check when you destroy the Transport Mothership when it follows you right after you obtain the Pirate Mothership. (In that case you get a funny dialog from Ternie before a forced game over, check out the "your stupidest moments in SW3" thread.