I’m unsure if this is an issue with allays or hoppers, but i cannot replicate the behavior without the allay, which makes me think it is an issue with the allay.
When an allay is trapped in the block space above a hopper, and the hopper has another hopper below it, the items will distribute themselves between both hoppers, as seen in the attached image. I thought this had to do with the allay’s hitbox being too low into the hopper, but after trying to separate them with a trapdoor, the issue persisted.
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Is the top hopper powered?
Is the allay dropping one item at a time, or multiple?
Assuming the allay is dropping multiple items at once or in rapid succession and neither hopper is powered, this is just how hoppers work. The top hopper collections a stack, then the bottom hopper pulls items from the stack in the top hopper at the same rate that the top hopper pushes items into the top barrel.