Put the summary of the bug you're having here

What I was expecting:
I used redstone programming to operate a brewing system that uses hoppers on all four sides of the brewing stand. Flipping a leaver activates a redstone torch and repeater cycling the bottom hopper and the side hopper filled with water bottles. The bottom hopper activates removing the 3 brewed potions. The side one is turned off stopping it from feeding potions. Flipping the lever back reverses the setting, turning off the bottom hopper, and turning on the side hopper feeding the water bottles in.

What really happened:
Instead the side hopper stops feeding water bottles. It will still feed blaze powder, however it will not pass bottles into the stand.

Extra Note
If I instead leave the hopper active and manually remove the potions the hopper will feed with no issues.

Steps to Reproduce:
1. Rebuild the structure from the 2 screenshots attached.
2. Flip the lever to the down position and wait for the stand to empty
3. Flip the lever back the up position and observe the potions not feeding.
4. If you place blaze powder in the hopper it will feed.

Extra note Based on what I have seen i suspect that the brewer when emptied by the hopper is not reporting "Empty" and preventing the potions from feeding.