Was using my runes of ascendency while waiting around in monoliths and ended up using my friends instead. I noticed after a couple tries that mine weren’t decreasing, asked my buddy to check if his weren’t as well and all of his were gone. We tested this a few times over the night and kept track before we upgraded and noticed it happening every now and then. I don’t know if this applies to affix shards (or glyphs) as well.
For now we’re just not crafting gear in multiplayer to avoid any problems.