I noticed today that the guild quest Sky Residence / Cloudy Storehouse had a problem. The quest is to place at least 1800 musk deer fragrance on a deposit. I tried a total of 4000 (two different attempts at 2000) and the quest wouldn't acknowledge them. Another player discovered that it worked if you placed onto a deposit that had 0. The ones I was using had at least 2k each. It worked for me too once I spread out the fragrance onto empty or near-empty deposits. It seems it doesn't recognize the action if there is more than "x" amount already on a deposit.
Now I have some deposits loaded up that are no where near hunters that will use them, but at least I got the quest done. And I guess it's ok to have a little backup of my preferred deposits.