This happened multiple times, finally I remembered to record it. I am still trying to figure out how to share the Xbox one clip directly with Bungie. As of now it's a youtube link.
I had four glimmer items, 2 house of banner and 2 axiomatic beads. While returning it to Cryptarch, a click on house of banner gave 200 glimmer and other one just disappeared. Same with axiomatic beads.
Exact details for Bungie support :
https://www.youtube.com/watch?v=xZxvTpYF7M0
Glimmer amount
1. Before approaching to Cryptarch - 8959
2. 4 items return, each of 200 glimmer - expected result : 8959 + 800 = 9759
3. Actual result : 9359
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Just a bug