I encountered this awhile back. You are absolutely correct, the NAV Zone does prevent 'some weapon' from being fired INTO IT. I've forgotten which one it is, but what you say IS TRUE.
The rest of the attacks work properly. I've just learned to work around it and, since it was only one, and I've forgotten which one it is.
As you no doubt know, the way to test it is to play that segment with, and without, the Nav Zone present. When it fires, and then doesn't fire, you will know which weapon it is.
But, what you said is true.