My problem is the same, although I never found it to be a big deal.
My guess on what you have found is a black hole, because you lose your probe to an unexplored sector when this happens.
If an enemy attacks it, you see their stuff before your ship dies.
So if you were getting your probe to travel on a straight path and they explored half of what they were told to, then that space after the explored stuff is "hidden fun stuff" (perhaps the ability to mark such places would be nice...)