I've collected some gear that's not getting registered as 'collected' by ATT, and occasionally it's resolved when I'd vendor it, but for some of it, the addon's not working as intended.
Mage: Collected several of the Darkshore prepatch gear from the world quests. As this is BoP, there shouldn't be an issue. The game itself registers the collection in the appearances tab, but the addon still showed it as uncollected.
Mail classes: I bought the Warrior's Leggings and Tunic, as well as the Infantry Leggings and Tunic (not in game currently, so the leg and chest pieces may be named differently; they're dropped from the two rares in Eversong Woods amongst others) off of the AH on a low level hunter. Appearances tab registered the addition when I equipped them, addon did not. I logged onto my 110 hunter (different server), and the appearance tab showed them; addon still showed them as uncollected.
I suspect this may have something to do with this gear being intended for plate classes before the proficiency changeover in WoD (mail wearing leather until level 40; plate wearing mail until 40), but the addon did register the collection of other pieces in the Warrior's set.

It's because you have addons or something blocking some of the API responses.

Do a ShIft+Click and it does a force refresh and checks the item.