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.