I don?t know if this realy is a bug, as it seems to be caused by myself doing something realy stupid.
I had a couple of colony ships returning from a 1.5 year or so trip, being down to like 3 of 5 spares, so, while on route to my HW, I ordered them to undergo a minor refit (I read only later, that the freight facility would provide a free major refit). The ships entered minor refit, but never came out of it.
After about 1.5 years, I deleted the ships and OOBed new ones.