Shift clicking does not work for all valid items for some slots. For example some items are valid for a slot and you can place them with your cursor but you cannot shift click them in the slot.
- Shift clicking empty bucket into fuel slot of furnace (to have it filled with water)
- Shift clicking non-smeltable item into slot for item to smelt of furnace
Based on 1.11.2 decompiled using MCP 9.35 rc1
The affected containers override the method net.minecraft.inventory.Container.transferStackInSlot(EntityPlayer, int) to not use the method net.minecraft.inventory.Slot.isItemValid(ItemStack).