When a Hopper is used to take finished items out of a Furnace, the experience from smelting is lost. I checked the GUIs of the furnace, the hopper and the output chest and didn't find the XP. I also tried disconnecting the output hopper and smelting a new item, and only got the XP from the new item.
Duplicate of MC-7046, please use the search function to see if your bug has already been submitted. Currently over 54% of tickets are being closed as duplicate.