The last couple of times I've loaded a saved game I have noticed that my custom designed ships seem to randomly change. I had some small and medium sized ships completely change what components and weapons/armor were placed on them. For example, on one small ship I had mass drivers equipped. When I loaded my game up again half of the ships of that type that I had produced had many of their "eye candy" ship components removed and the weapon system had switched over to a laser. This is EXTREMELY annoying, since it could cost someone dearly in a close fought war situation. Not to mention the result of the "mutation" makes the ships look crap!

Also, when I upgrade a ship and mark the previous version obsolete, many of my worlds can (and will) still produce the older design. This gets especially confusing when the ships are named the same. I often put "MkI" or "MkII" after the name, but I don't always want to (and shouldn't have to).

If it helps, I'm playing as the Iconians on the "Challenging" setting. Largest galaxy, tight star clusters and everything abundant with all other races present.