In the setup that is shown below the hopper with the water bottles doesn't forward items into the brewing stand, although it is unpowered and there is still room in the brewing stand.

This can be reproduced reliably and seems to not be dependent on position or orientation.

Notice, howerever, that the hopper is not stuck in powered mode because it still accepts items that are thrown at it.

How to build and reproduce

• Build the setup like shown in the pictures. Verbal step by step explanation:
  • Build a brewing stand with a hopper on top and on its side which point into it. Another hopper on the bottom to suck items out.
  • Place a comparator so that it faces the bottom hopper.
  • Place to hoppers facing each other behind that.
  • Fill these two hoppers with a stack of items.
  • Place blocks above of the comparator and the hopper.
  • Place a comparator, a redstone dust and a torch as shown in the picture.
  • Place a block and a repeater between the torch and the hopper that points into the side of the brewing stand. Set it on 4 ticks delay.
• Now fill the hopper on the side of the brewing stand with water bottles.
• Put a nether wart and a golden carrot in the hopper which is on top of the brewing stand.

Now one of two things happen: Either the hopper with the glass bottles doesn't transfer the items into the brewing stand, or it does. In the first case the bug is reproduced, in the latter case doing the following afterwards will always reproduce it:

• Fill blaze powder into the brewing stand to initiate brewing.
• Wait until the brewing has finished.
• Refill the water bottles in the hopper on the side.
• Put another nether wart and another golden carrot into the hopper on the top.

Now the bug should occur.