First of all, this is not a major issue. It does not prevent anything from working properly - at least to my knowledge.
When creating a custom inventory of type Furnace, if you take anything from the output slot, an error will be thrown into the console: it however doesn't prevent the item from being taken.
Attached to this ticket you will find logs containing the said error.
In case it matters, here is how the custom furnace inventory is created:
I made sure I was running the latest spigot version before creating this ticket.