As long as I know this kind of bug was introduced with the latest patch, what came along with the new DLC Dark Matters. I expect Amplitude to fix it starting on monday. And yes, the ships you see are Sophon design, not Nakalim. Another (display) bug.

Zu deutsch: Der letzte Patch hat einige Bugs mit sich gebracht, die kommende Woche gefixed werden (sollten).

I'm still getting this issue playing custom Nakalim game. Was it ever addressed?  To be honest I blamed a mod I was using but I think it's the game that's weirding out on this issue.