According to the wiki: "When a hopper is connected to an object to its side (for example a chest) and there is a hopper directly underneath it, items in the hopper will first 'leak' to the underlying hopper and only when that one is full will items be stored in the object to which the first hopper is connected."
This is true if the items are being fed into the top of the hopper, but if the hopper is being fed from the side, those drops will always be fed to the object it is attached to.
Reference the attached screenshot.
I have filters set up so that only magenta blocks can go into the magenta chest and only white blocks can go into the white chest. The orange chest should accept anything else. If I put magenta blocks into the top chest, they are correctly fed into the magenta chest BUT if I feed white blocks into the top chest, they will go to the orange chest instead of the white chest. If I put white blocks directly into the uppermost hopper over the white chest, they will correctly filter into the white chest.
Clearly the hopper code behaves differently if the items are coming from the side than if they are coming from the top.
Fixing this bug would allow for MUCH simpler and very reliable item sorting arrays.
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If you want more details and would like to see this thing in action, here is a video that breaks it down: http://youtu.be/h80qAGuJxkw
I'm not entirely convinced this is a duplicate of MC-6162, although it's possible that the root cause may be the same. If you say it is, I won't argue too much, but I would be sad if that were somehow fixed and this were not. 🙂
All hopper problems regarding a hopper being connected to a container with another hopper underneath are discussed in MC-6162.
Duplicate of MC-6162.