If you have a full inventory in game, it prevents you from being able to purchase ascendant shards from the cryptarch vendor, however it still allows you to buy the ‘weekly offer’ ascendant shards. It takes the prisms and the glimmer but it doesn’t give you the shards or send them to post master.
I just bought all the weekly offer capacity and can’t see the shards anywhere even after making room in my inventory, re-logging etc.
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I had the exact same problem... I lost my prisms. :(