Shift-clicking, while not very consistent to begin with, is extra inconsistent inside brewing stands, specifically with items shift-clicked out of the main inventory (the 3 rows of 9 slots in the middle). Follow these steps and compare them to how items would normally move:
1. Place a brewing stand and fill the fuel slot with blaze powder to avoid it interfering with shift-clicking preferences. This step is necessary due to MC-90718.
2. Put any item in your inventory (the 3x9 field of slots)
3. Open the brewing interface and shift-click the item: It will move into the bottom-right slot.
4. Shift-click the item from there, it will move into the first available slot from the top-left. Shift-clicking it again will move it into the last slot again.
Fixed somewhere between 15w42a and 15w44b.