Yeah this is a really 'imba'' bug. As to how did it happened is listed below.
1. I re-install GalCiv2 and patch the game to version 1.1 yesterday.
2. Started a new game yesterday and created a cargo-hull 'template' with all the necessary comestic visuals without any functional parts via the shipyard during the 1st turn. This template would allow me to upgrade the 'template' into different classes of ship such as colony, constructor and trooper and then saved it accordingly. So if I need a constructor ship with 3 speed right off the bat, i would select the 'template', add the construct module and 2 Hyperdrive+ and saved it as constructor mk1. So far so good. the sizes of all the components tally up 35+10+10=55.
3.Now in the 'ships avaliable' list in the shipyard, I have the original template and constructor mk1. I then played the game as usual upgrading the template with better stuffs and then saving it as a new ship whenever I have the tech for more powerful engines etc, Note that the template remains 'functional components less' throughout the entire game.
4. A while ago, i started a new game,went into the shipyard during the 1st turn and realised that my constructor mk1 which i designed yesterday has 10 empty space -45/55 with the same exact components. I managed to add in 2 more hyperdrive+. It seems that the hyperdrive now takes up 5 space instead of the usual 10. So now we have ourselves a 35+5+5+5+5=55 ship. I then deleted the 'constructor mk1' via shipyard and redesigned another constructor mk1 via the upgrade template step and the same thing happen.
5.And the best part of all, in the midst of typing this post, i went back into the game, started a new game and the bug is gone. Quited, re-enter the game a second time, started another new game and the bug resurfaced.