It looks like your using the Twilight beta, and this is a known issue. I think it is probably the same bug as reported here: https://forums.galciv2.com/?forumid=421&aid=173167
Please try turning off the "Use Enhanced Ship Rendering" option in the Options screen. You will need to restart the game, so make sure you save your ship and your game.
When you start up the game again, load up this game up and open the ship in the ship designer. Does it still look glitchy?
If not, please let me know.
If it is still glitchy, please zip your saved game (that has this ship design) and send it with your debug.err file to email@example.com. Please include a link to this forum thread in your message.
Thanks in advance.