I notice if you shift click in something into the furnace with both smelting slots full, the item you shift click in goes into some kind of hidden inventory within the furnace.
For example, two stacks of ore in the two slots, you shift click in one more stack but it disappears. then if you remove everything in the furnace and smelt, you are still able to smelt the hidden ore.
I ran a couple tests and see that if you shift click in just 1 ore piece and remove all items and smelt, it will only smelt that one.
Edit: known bug, furnace has 8 slots, but the UI just hides all but 2. as stated by @Jyanin just break the furnace to returive the items.