I found, later in the game, that almost all of my designs for ships that i've been using had dissapeared. These were all designs that i had currently being built by planets. Also when the designs dissapeared the planets that were building them kept with the production, though i couldn't assigns any new planets to build these designs as they no longer exsited.
I redesigned them and if i tried to use the same name the game would immediately crash. Much later on, like say 20 turns, i found that they magically reappeared.
If you want the save game before and after I can send it.
I had another bug along this line as well that happened just before this, all my planets stopped production and the governor screen wouldn't let me assign all planets to new ships until i restarted the game. IDK if this was the seed for this problem just thought i'd mention it.