I don't have any issues with my all Hunter team, as far as IWT with a hostile mob that I'm not facing.
And I don't have any form of unique set up for the Hunters.

In the Toolkit, the Hunters IWT exactly the same as every other team.
They're not in my "Melee ATG" (Action Target Group), so don't receive IWT as I spam my DPS key.
But if I push my manual IWT key, they do turn (the same as my Caster teams) towards the hostile and auto shoot it.

I remember Hunters having a few unique settings within the Warcraft interface.
And having some kind of an issue.
I didn't want them to auto assist and auto shoot, a new target... which was initially an issue with them.
But whatever my settings are, the Hunters act exactly the same as Warlocks, Priests, Elemental Shaman, Boomkins, etc, as far as IWT/CTM goes.