This affects Furnaces, Blast furnaces, and Smokers, but will use the furnace as an example:

1. Put in any amount of 1 type of item (iron ore) into the furnace, with sufficient amount of fuel
2. Have another type of item(gold ore) that would also smelt in your inventory,
3. While the items in the furnace is smelting, hold down shift and rapidly click the inventory item, as if you want to shift-click it into the furnace immediately after the original item finishes smelting.
4. Notice that after the original items supposedly finished smelting, the gui's arrow resets, but the last item is still in the input slot, and nothing is moved. 
5. only after exiting the gui and re-entering will all of the smelted items be in the output slot, and the new item will be in the input slot, waiting to be smelted.

Expected outcome:

The original item gets sent to the output slot, and the inventory item get shift clicked into the input slot of the furnace.

*unsure whether its due to clicking during a specific time but rapidly clicking usually is able to reproduce the issue.