Just sorta backing this up. Sorta.
Having dug through the api about this earlier, the issue isn't that it's not generating the ship or that the ship has been grabbed by the AI already, since the vanilla AI cannot (as far as I know) do this. Rather the error seems to be in the breadcrumb rangefinder.
Just to give an example of what I mean, here's my most recent mission:
Having looked through the mission hint system, if an object you're supposed to investigate isn't orbiting anything else, the system is supposed to give you vague hints based on the objects proximity to the star. Something in the "Heart of the System" should be within 5000 units of the center. On the system map, each grid square is 2000 x 2000, so the derelict I was looking for
should be within the circled area plus, I presume, some wiggle room to account for the stars size. As you can see though it's kinda not.
I suppose it's possible that this could be the result of a mod messing things up some, but the only one I can think of that might cause this issue would be Tartiflette's Unknown Skies, and I have no idea how it would do that since right now all it does is add a bunch of different backgrounds and planet types.