The Original Post described a problem with loitering ships, something I've had as well. My civ fleet ground to a halt earlier, ticking me off. Then I realized a candidate problem:
I had uneven supply\demand orders. Earth was supplying 5 mass drivers. Penumbra and Corundius were demanding 2 and 3 automated factories each. Nothing happened, civs collected at earth.
I wiped out the uneven orders, and the whole fleet took off on their missions.
Perhaps this is in fact a bug worth bugging out about?
Yours sounds like it's worth logging a bug for. In the original post, I think it depends on the orders. If he clicks "Show Next Order" on the Display tab of the F3 screen and they show "Unload trade goods at X" but there's nothing actually on the ship, then I'm pretty sure it's a bug. If it says "Load trade goods at X", then there's a good chance that it's WAI (Working As Intended) - there's just nothing to pick up at the location they're at, so they go looking for stuff at a different location (I think I remember this being part of the civie AI). It's probably still ok to mention in the bugs thread to confirm WAI, he should just make sure to describe exactly what the orders look like.
If they're really ignoring contracts at the spot he mentioned (or within 4 jumps), then yes, it's probably a bug.
John