I had to stop using multiple designs cause of this, it got really annoying when the list filled up (accessing from galaxy map) with obsolete constructs.
Also my new designs get faulty appearance (If I had Cruiser Mk I from a previous game and I made a new Cruiser Mk I in a new game, the new Cruiser Mk I would appear to have lasers etc when I actually fitted it with plasma)
What I did to "fix" this is, I went into my documents folder (WITH Galciv 2 running), deleted the ship designs I didnt want and saved the game.
If you delete them while not running your save game, all designs get put back into your ship design folder once you load the save.
But if you load the save, delete the designs and then save again, yer good.
So now I only replace all my designs (i.e, instead of making Mk I, Mk II etc I now just replace Mk I all the time)

Just wanted to reply that I, too, have encountered this bug many times. If I name a ship as a name that already exists (not sure if it was available at my present tech or not), then I would get the pop-up warning about not naming upgraded ships the same name. Then on the list of ships to build, the exact same ship (same name, same stats) would appear twice.

This problem has now been fixed for the next update.