I put 8 iron ore in multiple furnaces and after collecting the 8 iron ingots from the few that had finished already I watched the last one finish smelting as I waited.
When it finished the fire animation turned off like normal but there was still a single ore in the input slot, and 7 ingots in the output slot. I collected the 7 iron ingots and they went to my inventory as expected. I then clicked on the ore in the input slot and it went into my inventory as an ingot.
Are you on a server or in a singleplayer world?