When I upgrade a ship design and give it a name that WAS in use in a previous game it will botch the ship, giving it extra components, different hull, etc etc.
To be clear, it happens, If I take my "surveyor 001" ship. upgrade it, and save it as "surveyor 002" where I did NOT have a surveyor 002 in my ship list. But I did have a surveyor 002 in a previous game.