If a hopper has an item (jungle sapling) thrown in and a chest (Full of stacks of 1 jungle sapling) near it, it will ignore the chest and go to the next hopper. However, an item that has been placed manually will go into the adjacent chest. This is NOT a duplicate of MC-6162 because that issue does not feature this bug. Please do not flag this under that duplicate.
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For each stack, the first item goes in the bottom chest, the second to the top, the third to the bottom, etc. Resolving.
Unable to reproduce. Items always go into the lower hopper.