Now don't shoot me for posting this, since we all know if it, but if this were fixed it would make me buy Twilight of the Arnor in an absolute heartbeat.
Since the original version of GalCiv, the shipyard pieces have been... imperfect.
Nearly every piece has minor flaws in their design and hardpoint attachment. For example, the 'big flat beam' piece that is integral to any starship design, has a very noticeable 'curved' shape in it due to a modeling defect. Other parts, when built symmetrically, do not line up properly and end up giving ships a lopsided look.
I know it's a minor issue but it's something that has always been a major pet-peeve of mine.