Hoppers put going from one furnace to another dont work, configuration below, going from cobble to smooth stone
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The hopper is pointing into the side of the furnace and therefore trying to put items into the fuel slot. In order to fill the top slot, you need to have the hopper above the furnace.
Side input is for fuel. That configuration is attempting to put smooth stone in the fuel slot, which it won't go in. To transfer from the output slot to the input slot, the hopper needs to be inputting into the top of the second furnace.