Sebastian Schieß

It "reproduce" some times on multiplayer servers.

First: create a stack of renamed items over the anvil.
Second: Split the stack into two or more smaller stacks
Third: Put a hopper on another hopper (facing away from the lower hopper). Block the lower hopper with an redstone torch below it.
Fourth: Put the small stacks inside the upper hopper with leftclick-hold and drag-over.
Fifth: Try to put another smaller stack of the renamed items on the existing renamed items in the hopper.

Result: 90% of trying switches the items in hand with the items in hopper (not stacking, replacing). I'll try to make a video of it.

THAT is the issue, i found. (tried to build a item sort machine with hoppers. check out the tutorials on youtube. the "placeholder"-items (2, 3, 4 and 5 slot) i ever renamed on anvil to prevent accients.)

I hope, my english is good enought for it to reproduce the issue and helps to fix this bug.