The funny thing is, I have also been getting this with ships that I've saved during the same game! I'll create a ship, and when I go back to upgrade it, it seems random wether or not it's messed up, but I've only seen this on ships I've created like two savegames ago. Also, something weird happened recently, I loaded up a save game, and I only had 4 designs in my shipyard! Yet one of the designs that was missing was still being produced! This was a autosave.