Having exactly one empty glass bottle in a hotbar slot and using it on a water source block deletes the bottle.
How to reproduce:
Give yourself an empty glass bottle.
Put it in your hotbar and switch to it.
Use it on a water source block.
Expected result:
The bottle would turn into a water bottle.
Observed result:
The bottle is removed from the inventory.
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The bucket bug is tracked at MC-275757, so I've made this report specific to bottles.
MC-275757 already describes the issue with buckets.