In the latest patch the way legendary gems are stored in the Inventory was changed…
Legendary Gems will now be sorted into stacks based upon their quality, rank, and if they can be sold at Wynton’s Grand Marketplace.
Prior to this update, where legendary gems did not stack, it was possible to individually lock / unlock legendary gems. Since the update, it now seems the lock / unlock affects the entire stack, i.e. you can either lock all of the gems in the stack, or unlock all of the gems in the stack, but there is no way to unlock just some of the gems in the stack.
So, the scenario I had this morning was upgrading a 2-star gem from Rank 5 to Rank 6. This upgrade required another Rank 5 and a Rank 3. Prior to this morning’s update, I would have had one of the Rank 5’s locked (the one I’m upgrading), unlocked the other Rank 5 and the Rank 3, then done the update and auto-filled. Since the update, I now had to unlock the stack of Rank 5 so, when I clicked to upgrade, the Auto-Fill didn’t work, as it didn’t seem to know which Rank 5 should be upgraded and which was being used as the spare. I had to manually select 1/2 of the Rank 5s from the crafting window.