The bug

When a brewing stand is unloaded, such as saving and quitting in a singleplayer world, the cycle is reset to the start. This includes consuming another blaze powder.

For example, if you are adding nether wart to a water bottle, and it was almost done the brewing cycle, then exit your game it will be back to the start when you join back. It does not restart when the chunk is unloaded/reloaded by moving around in the world.

Issue has existed for a long time and significantly hurts redstone automated brewing contraptions (close world while auto brewing = machine broken).

Code analysis

Code analysis by marcono1234 can be found in this comment.