1) The move together option, seemed to work for a group jump most of the times, but once when I was jumpin in system with dual capital ships it didnt work: http://naia.b-especial.com/FOTOSnaia/Hyperjump.JPG
2) The neutron bombers, had for several times an unsual lag delivering their payload, ending numbers 1 trough 4 to see the respective time diferences that was +- around the time when I saved the game.
http://naia.b-especial.com/FOTOSnaia/NeutronLag1.JPG
3) Starbase graphics are in the wrong place AFTER loading a saved game,
http://naia.b-especial.com/FOTOSnaia/SpaceStation1.JPG and
http://naia.b-especial.com/FOTOSnaia/SpaceStation2.JPG
4) A in-construction starbase has its shields fully loaded with TEC cap ship's help.This was exploited by me, jump a constructor and a few caps and voila, imba starbase shields are up now we wait for it to pump up.
http://naia.b-especial.com/FOTOSnaia/SpaceStationShields1.JPG and
http://naia.b-especial.com/FOTOSnaia/SpaceStationShields2.JPG
5) Panic. To imagine every single system with those and carefuly microing the waypoints for a safe path.. nightmare time consuming 
http://naia.b-especial.com/FOTOSnaia/Panic.JPG
6) Best of the best, maybe this is not a bug? Starbase atacks mines that are in range, ending numbers 1 trough 4:
http://naia.b-especial.com/FOTOSnaia/StarBAtacksMine1.JPG
7) Zoom in and out errors, half the ships show up, sometimes... sometimes not, here is folder with pictures:
http://naia.b-especial.com/FOTOSnaia/Zoom/
8) In this game I was playing, there was two pirate planets on each star. I cleaned out mine, and let the bounty increase so I could test my defenses. Since the other pirate base on the other star as up and runing it should be ok. They *never* atacked.
here is saved game:
http://rapidshare.com/files/183345368/saved_game.rar