Activated hoppers are allowing items to pass through.
Steps to reproduce
The issue occurs under the following circumstances.
Place three hoppers in a vertical column (see first attached image).
Power the middle hopper with a redstone block.
Place items in the top hopper.
Observe that the items pass through the middle hopper to the bottom hopper.
Alternative ways to reproduce
The issue still occurs under the following circumstances:
Placement of the hoppers on chunk boundaries or within a chunk.
It is not sensitive to the type of item being transported.
Middle hopper powered by a repeater or redstone torch.
Middle hopper powered indirectly.
Middle item replaced with a chest (see second attached image)
Top hopper powered instead of the middle hopper.
Middle hopper is powered in all four directions.
Does not occur
The issue does not occur under the following circumstances:
Both top and middle hoppers powered
If the hoppers were placed prior to 1.2.x
Linked issues
is duplicated by 2
Attachments
Comments 3
The diagram is a simplified illustration of how to reproduce the bug.
The behavior of a hopper is that when it is activated it should be disabled and therefore not allow items to pass through.
The diagram illustrates that this is not the case.
And yes, the behavior also manifests with a chest as the middle part of the chain.
I'm not sure how this issue has been overlooked for so long; I apologize for that. However, this works as intended.
What's happening in this case is that the middle hopper is being disabled, but the top hopper pushes items into it and the bottom hopper pulls those same items out of it. When you have a vertical stack of hoppers and you want to disable item flow through them, you must deactivate both the one where you want items to accumulate and the hopper below it as well.
What you've done here does have an effect, though: Because the middle hopper is not pushing and pulling, items lodge within it for 1 tick longer than they normally would, so the overall item flow is slowed by 50%. You can confirm this by timing how long it takes to feed a stack of items all the way to the bottom hopper.
Based on your image it's a design flaw. The top hopper is pushing items into the middle hopper, while the bottom hopper is pulling them out. The middle hopper doesn't need to do anything. You could replace the middle hopper with a chest and this would still be the result. To fix it point the top hopper in any direction but down.