You can't put any items that burn in the bottom of the oven. Only items on the top can be put in but not retrieved. If an item is cooked because some existing ovens already have fuel, then you can't retrieve the cooked item. This was since the last update that I just did on June 5th 2013.

As you can see in the attached picture, I have cooked a shiny ingot but I can't retrieve it.