This occurs when there is a stack of multiple gems in a storage chest. If you try to transfer a single gem to inventory rather than the entire stack, it is removed from the chest but does not appear in your personal inventory.
If you transfer the entire stack back and forward it works fine, but removing a single gem from the stack in storage causes it to vanish completely.
Just to add, I have been able to recreate this repeatedly. It occurs when you transfer single gems, but have your inventory open on a page other than the “resources” page the gems are supposed to transfer to. The gems are removed from storage, but if you then flip to your own “resources” tab they are not there, they simply vanish into the ether.
Can someone have a look at this please?