^{Update by Mega_Spud:}
Summary:
Empty glass bottles can be placed in a brewing stand using a hopper, but they are also changed when brewed alongside potions/water bottles, meaning that they can no longer be stacked with other empty glass bottles.

NB - In the Java Edition, empty glass bottles can be placed in a brewing stand directly or via a hopper, but are not affected by the brewing process.

Steps to Reproduce:

1. Place a hopper directed into the side of a brewing stand
2. Place two water bottles and an empty glass bottle into the hopper, so they go into the brewing stand
3. Place nether wart and blaze powder fuel in the relevant brewing stand slots
4. After the nether wart is brewed, remove the empty glass bottle and attempt to stack it with new glass bottles.

Observed Results:
The glass bottle is affected by the brewing process, and can't be stacked with other glass bottles.

Expected Results:
Empty bottles can be placed in the brewing stand (as they can in Java) but they should not be affected by other potions being brewed at the same time.

Screenshots/Videos attached: Yes
glass_bottle_brew.mp4

Notes:

Original Description:
So I've realized that hoppers can put glass bottles into brewing stands. This wont actually start the brewing, but if you add a water bottle then the brewing will begin and it will brew the glass bottles and the water bottle. When I checked the glass bottle's NBT data it showed they had the justbrewed tag.