I don't know that this constitutes a bug, but if I could have one and just one change -- it would be to make the "guard" ship/fleet command actually do something besides 'Sentry+lose remaining movement'.
I'm sure I'm not the only one that isn't playing on a dual core machine. The endgame drags excruciatingly - but I stick with it because I do love the game. However, the 'waking' of units set to 'Guard' has to be the most keyboard pounding, profanity inducing, mouse crushing issue I have in GC.
Guard. Means. Guard. It should be the equivalent of 'Fortify' in other 4X games. It means do not awaken for orders when a large piece of space dust floats by. It means do not get bored and request orders. It means sit there and do nothing except respond to attacks unless I @#!@$@! tell you to do otherwise. If I want you respond to someone entering a quadrant, I will use Sentry.
Especially late in the game when starbase fortifcations are worthless -- I have fleets sitting atop bases protecting them. I normally have more than a dozen starbases. When workign through a 20 minute turn, nothing annoys me more than having to reissue orders to a braindead captain that can't follow them.
I honestly close my eyes and dream of the most savage and horrible executions I could subject these jumpy loons to. I imagine tying them to positronic torpedos and firing them into the sun. I imagine run a hook through their body and fishing for space monsters. I imagine using them to test to see if those 0 PQ planets truly are "unihabitable".
For my sanity, please, I beg you.... make Guard actually work properly.