Several appearance items I have added to my collection from Marks of Honor are showing as not collected. So far I have noticed:
All of the Warmorngering Combatant cloaks and drapes, Notorious Gladiator's Silk Shoulderguards.

@gbrage @Goldenshacal

I was able to determine after doing a faction change that there appear to be separate horde and alliance appearances for Warmongering Combatant's capes. ATT doesn't appear to be able to distinguish between the different factions for these items and thus if you don't have both, it will show as not obtained. After the faction change was completed and I purchased the alliance equivalents, they now appear as owned / complete.
The only one other item that still persists in not showing as owned is the Notorious Gladiator's Silk Shoulderguards under the Ensemble: Notorious Gladiator's Cloth Armor. I own the complete set and it is still showing as the Shoulderguards not being collected. I have tried purchasing the Ensemble again to relearn, but the game tells me I already own the set. Tried this same method of purchasing after a faction change to determine whether different factions have a different appearance for this 1 item, however it wasn't the case and still tells me I own the set but ATT showing as missing just the Shoulderguards.

Possibly the cloaks are missing some faction restriction and this showing when not collectible by the current faction.
As for the ensembles... More tickets to Blizz. We can't force the game to give you what it was supposed to when learning an ensemble or having appearances already granted via individual pieces. This has been a Blizzard flaw with ensembles for ... always.