When making a sorting setup with hoppers and chests, I use hopper upgrades so items can be filtered from the main hopper line. But when I use a filter upgrade, the hopper upgrade ignores it and let's all items in which aren't on the allow list.

That actually works as intended as hopper has its own filter and filter upgrade is supposed to only work with hoppers/pipes attached to the storage. I can see how it may be confusing in this case, let me think about whether I want to change it, but I leaning towards keeping it the way it is otherwise there would be inconsistency with other upgrades like pickup and magnet where I definitely want to keep it so that they have independent filter.