This happens only with Bio Fuel in combination with Silver or Gold.
It doesn't matter what type of silver ore or gold ore it is.

I figured it out. The bug is actually that it automatically outputs stuff when its supposed not to. Thank you.

Edit: Actually this works how it is supposed to. At least a the current implementation.
Basically your "Slots" are configured that they can't export up.
Thats the problem.

Yes the machine is exporting even so the slots are not allowed.
But the export upgrade deals with Items that aren't in the "Inventory" yet. In other words then the machine settings apply.
And these allow into all directions.
This was a intentional design to keep the code a lot simpler.
Yes it sounds dumb but its this way.