I was using a small supersmelter, and I was smelting exactly 18 stacks of raw copper (2 stacks of block of raw copper), while it was running I decided that I wanted to change how the output hoppers were arranged as I did this it looked like I didn't get back as much copper as I thought I should sure enough when all of the furnaces finished smelting I only had 15 stacks and 1 copper ingots in the output,

I'm not sure what cause this but my guess is that either the problem occurred when I broke a hopper that was moving items or, when I quick moved the the copper ingots into the output chest that was having items put in it

I'm sorry if this is vague but there was a lot of moving hoppers around, and picking up items. so if there is a problem it could have occurred in many different ways.