Non-fuel items can't be placed in the second(bottom) slot of furnaces. It may not be a bug but a fix, but it is not that great because many use this method with /testforblocks command for two-item "crafting".
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I know this was possible, even if it would not smelt, but in this snapshot you cannot even place a non-fuel item(I tried even to do it with a hopper).
WAI. This has been possible since I can remember. The furnace will not smelt though.