Smelting items isn't 100% efficient (only on laggy servers?)
Whenever smelting large numbers of objects (such as a stack of iron ore or the like) I have found that typically one or two items remain unsmelted despite inputting the correct amount of coal. This could possibly be caused by server-side lag.
To this end, there is a possibility it may only be reproducible on minecraft servers with server-side >50 ms lag.