Just a short update on this issue:
my ticket got updated, the devs (or Derek I guess, thx for the help) found out that I somehow managed to create 2 constructors with the same ID. This should not be possible.
However, so doing stuff with these constructors with the same ID will make the game crash. Upgrading, deleting or making other interactions - even if the NPC does (like attacking them), the game will crash. My solution right now is sending the bugged constructor to one of my planets and do nothing with them, that is fine (you need ofc a savegame where you did not build a starbase and modules with the bugged constructor, if you already did you cannot load that savegame).
My problem with this solution right now is only that the NPC is attacking my planets and if the constructor is also there I get the crash - so I have to run away with that bugged thing , but that is the best thing you can do right now if you have this issue.
Current opt 1.02 is not solving the problem if you have already made a bugged constructor. But as I understood someday there will be an update for this issue. Right now the question is how it was possible to create 2 ships with one ID. My guess is maybe I did somehow build too many constructors with different shipyards at the same time and also used Ideological point Constructive (gives 3 const instantly) and there things got mixed up.