NOT impressed - max amounts and quest quotas

I farmed all over Argus in search of the required 50 Pristine Argunite to clear a quest-blocker from my queue.

When I picked up the final thirteen items from a chest, I was told I could not pick them up. I had reached the 2,000 item limit for this Item, and it only allowed 49 of the 50 required for the quota.

If I cannot satisfy a quest with items previously obtained, but those same items prevent me from satisfying the quest due to this ceiling, that is one thing.
But the nail in the coffin, the slap in my face, is that once I spent some of my Pristine Argunite and returned to re-fetch the chest, it is missing. Is has been marked as found, and no longer appears.

This appears to be a bit of a double standard. I think the correct way to handle such a problem is to return the entire stack of loot to the chest and leave the chest as available/findable. But perhaps the problem is that the chest contents are rolled upon open. If so, then allow players to exceed the quota ONLY if they were BELOW the quota before looting. THEN block any additional pick-ups of the over-quota item.