Found when attempting to craft hoppers via shift-clicking the recipe in the crafting menu while I had a full inventory.

Repro steps:

1. In your inventory, have 1 stack of Chests, 3 stacks of Iron Ingots , and then fill the rest with whatever random items (it just needs to be full). 
2. Go to a crafting table and drop 2 stacks of Iron Ingots on the ground in front of you. 
3. Open the crafting table, then shift-click the Hopper recipe. This will put 38 Chests and 190 (38x5) Iron Ingots into the crafting table.
4. The 2 stacks of Iron Ingots you previously dropped (plus 2 Iron Ingots left-over from the first shift-click) are now in your inventory, along with the remaining 26 Chests.
5. Finally, shift-click the Hopper recipe again. The result is that, in the crafting table, there will now be 1 stack of Chests, but just 3 stacks of Iron Ingots, rather than the expected 5 stacks. Now exit the crafting table, and you’ll see that 2 stacks of Iron Ingots have completely disappeared.

I’ve tried this several times using these exact steps and the result has been the same each time. I set up a Chest full of stacks of Iron Ingots and repeated steps 2 to 5 several times, and when I was finished, the Chest was empty but I still just had 1 stack of Chests and 3 stacks of Iron Ingots.

I’ve also tried this with a few other 2-ingredient items, e.g. Clocks, Compasses, but it only seems to happen with Hoppers.