Holding a glass bottle and right-clicking a water source gave me a water bottle for a moment before changing instantly back to glass bottle.
Holding a glass bottle and right-clicking a water source gave me a water bottle for a moment before changing instantly back to glass bottle.
You must have mis-clicked, it works for me.
You might have been holding a stack of empty bottles, once you fill one it gets relocated to an empty part of your inventory. Maybe your inventory was full?
Remember to test your own bugs before reporting.