One time in my testing world, I had two hoppers pointing into each other. When I put an item in, the item disappeared. I broke the hoppers and replaced them, and no items fell out. I tried putting in another item. It didn't happen again, but the item ended up reappearing out of nowhere.
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We're tracking this issue in MC-119971, so this ticket is being resolved and linked as a duplicate.
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Cannot reproduce in 20w29a, does it still happen?