I don't know if this has been addressed, but I confirmed with my clan that it is happening with them too. Say you do PoE challenge and get 6 of the little white triangle things that you turn in to Cryptarc (sorry for spelling) for 200 Glimmer. I've noticed at the Reef that when I have 6 or so it only allows me to claim a few of those and then switches to decrypting engrams. I looked in my inventory and they just disappear.
I've heard it could be showing more than we actually have, or there is a bug. When I hit max Glimmer they also just disappear. Again, this may have been addressed but wanted to see what the community knows or has seen on this topic.
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This has been a glitch for some time. If you notice before turning in the Glimmer items, there are doubles of the same item, making it appear that you have way more to turn in then what you actually have.