The bug

The changes to the hitboxes of a hopper affect items that get thrown onto the hopper from the side. In the picture I provided (2017-12-02_19.53.13.png), you can see the bug in action. When you throw an item in from the top it gets pulled down to the lowest hopper; no problem. When you throw an item in from the side, like I did, they just don't get picked up. When you break the hoppers from the top down the items get picked up and end up in the lowest one.

Code analysis

TileEntityHopper.captureDroppedItems(IHopper) first checks if there is an inventory above it. If so, it will attempt to pull an item from it and then return true or false. If there is not an inventory above it, it will try to find item entities and put them in its inventory.

Since there is an inventory above the hopper here, it never checks for items above it.