It appears that if your consumables are full and you have ether seeds, black wax idol, resupply codes, etc. active they will not give you any glimmer upon killing the corresponding enemies. Also glimmer is not received upon killing a yellow health bar enemy.
Simply dismantling or freeing up a slot in the consumables solves this issue.
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Personally haven't seen any glimmer in a few days even with out having one active. Driving me nuts when trying to infuse or max a weapon/armor lately. Thankfully still getting green items to junk and make glimmer that way.