Thank you for the report, would you be kind enough to share your save file of the game? To be clear you're saying it would be more helpful if the ships changed to all of the ones in the same sector before moving to the next correct?
This is a common problem with most if not all games.
It happens in the Civ games and GC I-III as well it just is not as irritating.
Many people complain that the jump from unit to unit is random, I believe that it is mostly by the order of build also.