Using:

Minecraft 1.10.2
Skyfactory 3 (3.0.15)
Hatchery 0.3.21

I have a shredder with a hopper on top feeding feathers to the shredder, I realized that even if the shredder had 64 feathers already the hopper was still counting down the feathers (as if it was still putting them into the shredder) basically, even if the shredder is full, the incoming feathers get voided, it also happened using enderio item conduits (only at a much faster rate though).

That be an issue.. I will check it out.

This issue was prolly fixed in later versions. and I haven't really made any updates to 1.10.2 So cant promise I will get back to this atm. I know for a fact that skyfactory 3 shouldn't be getting anymore updates. You may, You may try updating to version 0.3.22 and see if that fixes the issue.