I was trying to make an automatic brewing setup, so I made a water step system where I had three dispensers shoot out water bottles, step up and another dispenser with nether wart, step up and another dispenser with sugar, and one last step up with another dispenser with redstone dust. When all dispensers are activated using a redstone signal, the dispensers shoot out the ingredients and they start going down the water step system a hopper. They land somewhere in the middle of the hopper and get absorbed by the hopper. The problem is that some items get sucked in twice, duplicating the item(s). The hopper is then setup to go into a brewing stand.

I expected the items to go into the hopper and subsequently into the brewing stand.

What actually happened is that sometimes items will go into the hopper and then reappear on top of the hopper again and get absorbed again.

Easiest way to replicate, load map and press the button linked to several dispensers, then check hopper, brewing stand, 2nd hopper and check the last chest, there will probably be two of each item.