Bottles get deleted when drinking a potion when there is more than 1 in a slot.
Reproduction steps:
Use this command:
/give @a potion[potion_contents={custom_color:8439583,custom_effects:[{id:jump_boost,duration:600,amplifier:1}]},custom_name='["",{"text":"Potion","italic":false}]', minecraft:max_stack_size=5] 5
Clutter up your inventory, there must be no empty slots
Switch to Survival
Drink the potion
→❌ Notice how a potion has been used, but the glass bottle just disappears
What I expected to happen was the glass bottle being dropped as an item.
Can confirm in 1.21 Pre-Release 2, 1.21 Pre-Release 1, 1.20.6 and 1.20.5.