Actually I think this is one area that was cleaned up a bit, but it still confuses some if they try and apply the rulings from the previous set. In the first rulebook, "touching" was not a defined state as it is now.
If a ship's manoeuvre (other than a stop) is insufficient to clear another ship, the overlap still occurs even if the ship slides back down the template to it's starting position. This would still result in an overlap and leave the ship touching because the final position would have been on top of another ship's base.
Let me try again.
In turn 1, A moves after B, overlaps B, and A and B end up touching.
In turn 2, B tries to move, does not overlap A, but overlaps C, and does not move.
Also in turn 2, A tries to move, but overlaps D, and does not move.
As currently ruled, A and B are still touching. They did not overlap one another this turn, but they are still touching, because they have no "moved away."
That's the mess (one example of it). The rules would simply be cleaner if you're only touching ships for which there was an overlap in the current turn. Unfortunately, the "move away" language in the rule-book has been ruled very literally.