Basically what seems to be happening is that the starship designer is throwing out duplicate names when it shows you the list of ships you can upgrade or otherwise manage (delete, obsoleete, etc.), whereas the build list from both the planet screen and from the main interface when highlighting a planet includes duplicate names.
So, I run into this situation constantly. In each game I start, I tend to upgrade the Colony Ship to a Colony Ship I, then later to a Colony Ship II, etc. I also do this for other ship models, such as the Constructor, Scout, etc. Since each game I play I tend to find an opportune moment to upgrade the given class of ship at a different time, hence having different tech available when I do so, I end up needing to create very different Colony I vs. previous Colony I ships. When I do so in the ship editor, it warns me that I shouldn't use the same name for upgrades. Howver, what am I suppossed to name this ship? Am I going to recall every game that I've created, and come up with a random suffix to try to avoid name conflicts? Plus it is just natural to name the next version of a ship I, II, III... or mk1, mk2, ...
So, I confirm that I wish to "replace the existing design" but what seems to really happen "under the hood" is that both designs exist. So when I go to build a ship, assuming I have the tech for some previous upgrade model I've designed in some other game, I end up seeing 2 or even 3 or more "Colony I" ships. Its a real pain! I would have preferred that, as the confirmation dialog *seemed* to indicate, that the new Colony I should REPLACE the old one, and I should never again see some other version of "Colony I". Alternately, if its going to insist on creating duplicates, then the ship editor needs to show the full list, so that I can obsolete the one(s) I don't want in my current game.
Clearly this is a bug, albeit not a crash bug.
Thanks (I'll post save games, or whatever, upon request)