The bag doesn't get sorted at all when clicking the clean up bags button if you have a hunter with any type of ammo bag equipped. I disabled all other addons just to make sure it wasn't something else, and it still happens for me with only the GW2 UI loaded.

I also tested by removing the bag from the bag slots and just having it sitting in my inventory, and functionality returns to normal.

Edit: This is for Wow Hardcore, not sure about other versions