The shredder only allows upgrades in its upgrade slots, but the input space accepts any item, or stack of item. (Luckily it doesn't shred anything you put in there, though)

Secondly, and related, items, including feathers, can only be shift clicked to be removed from the input slot. Left clicking to pickup items does not. Upgrades, once again, work great, and do not exhibit this problem.

is this 1.10.2? It has been an issue, and hasn't changed because it needs a partial rewrite.

This is 1.10.2, specifically the skyfactory 3.0.15 setup.

I didn't see any changes to the shredder UI in your 1.11+ notes, but I should have mentioned it.