I noticed that, too. It is especially stunning, when you see, where these ships were/are actually headed. I had situations, where the hyper wave decoder told me, that the target area was southern America, while the supply ship actually landed in Europe. Such things happen, and I know they didn't always. Of course, when patrolling over such a supply ship, you can stay there forever and never find any base, as the base is actually placed somewhere completely different. Only thing I am not sure about is, whether this happens, when you destroyed a base while the supply mission was already scheduled or something like this. Or whether it simply happens, no matter what you did before.