I was designing a potion brewing machine and noticed that the ingredients were entering the potion stand in the wrong order. For some reason in the middle of the way the ingredientes order messes up. I did some tests, this bug occurs even in a straigth line, just block a hopper in the middle of the way (power it) and there is a chance he will already will change the order of the itens, if not then at end of the line.
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This is intentional behavior, see MCPE-28890.