I'm using Fab's list builder while at work, so I don't have the physical card in front of me right now. But, here's my quandary:

Special Rule: A player gains 1 victory token when an opponent's ship is dealt at least 1 damage card from moving through or overlapping an obstacle.

In the rules it states that only overlapping at the end of a move triggers the overlapping effects. The way this is worded doesn't seem to change that. Am I missing something?

Nope.

So currently only half of the triggering conditions for the special rule are in play, until another game card (which currently doesn't exist?) says a ship takes the overlap penalties for moving through an obstacle as well?

I think it is more lacks wording on the objective card. Ending your move on the objective could be the same as moving through. I mean the ship is considered always moving so ending its move on and being hit by obstacles IS moving through them...

Although...

Moving through could mean just that. If the ship's course takes it through the obstacle you score the VPs but only suffer ill effects if it overlaps when movement has ended.

Though moving through by itself would never cause damage, right?

Because:

Ships and squadrons can move through obstacles

without issue; only the final position of the ship or

squadron matters.

Yeah, something in the wording is definitely off

Correct.

Is this referring to the Dangerous Territory Navigation objective?

That card makes no reference to moving through, only that you can obtain a victory token when a ship overlaps an obstacle.

I was refering to this:

http://starwars-armada.wikia.com/wiki/Navigational_Hazards

Though now that I think about it, I don't know where that card came from. Unless it was in a preview and got scrapped before release.

Possibly, it certainly wasn't part of my core set.