https://www.youtube.com/watch?v=KT8KPoF3jx0

We created a sorting machine design based on the one in the video above. It works in single player vanilla Minecraft and it works on the old CraftBukkit 1.7 version without plugins, but it does not work with Spigot's 1.8 builds without plugins.

The problem seems to be with hopper logic. In the setup shown in the video, which is the same setup used in the system we tried when we came across this bug, hoppers are connected sideways in a chain across the top level while another set of hoppers below those which are not connected to each other contain 21 stackable items. In vanilla Minecraft and in older CraftBukkit versions, items will pass through the top hopper chain and when the hopper below them contains at least one stack that the item can stack with (i.e. an item of the same type), the item will pass into the hopper below rather than into the next hopper in the chain. However, in Spigot, this only happens sometimes. We have yet to determine whether it depends on the location of the unit or the type of item, but certain items sort consistently with sound hopper logic while others consistently continue through the chain when they should drop out. We have yet to find any pattern as to those tendencies, but they are consistent with the position and item type for that unit of the sorting machine.