Occasionally when you gather, the item shows up in the loot window but isn't looted. To get the item, you have to re-gather the source again. Needs a bit more investigation. Not a consistent bug, happens periodically.

@AeroScripts This happened yesterday on the Kolkar's Booty chest while we were questing, and just looking in the chest consumes the key. You can't look again. Doh, should have had you level skinning. (=

This happened in ZG when I was trying to skin crocs.

Solved this. Was trying to skin 60 level mobs and sometimes it fails during raids. Derp.