If I remember correctly I saw a thread on this forum about ships dissapearing after a time even when the mission was not complete.
Could there be a correlation? Maybe when Sir Emi fixed this that all ships came back?
Otherwise you found a Bermuda triangle in space JJL...
I remember that happening. That was with hijackings. The ones that seem to be mostly plaguing these smaller systems are nest. Could be some bug or whatever keeping them around. Most of the time it doesn't present a problem to me but I am sure there are some it does.