It’s pretty simple. Hoppers can’t transport items upwards. Hopper Ducts Mod for Minecraft 1.9.4 Mods adds ducts, which can attach to hoppers and send items in any direction. This mod also now adds Grated Hoppers, which can filter items.
Download link: Hopper Ducts Mod for Minecraft 1.9.4/1.8.9
Read more: Minecraft 1.9.4 Mods