Oops, this is a duplicate. I couldn't find anything on it before issuing this, but after searching a bit better, I found MC-12363.

When making quick movements with the mouse, there might be disagreement between the client and the server regarding item events. For example, when using a glass bottle on water after a fast movement, or using a water bucket will make the water momentaneously appear in the incorrect location. Block placing seems unaffected by this.

I found this bug while working on a mod of my own, as this issue affected some of my items, but then I realized it affected many items in game.

What I expected to happen was...:
The glass bottle would appear as empty and no sound would play, or it'd be full and a sound woud play.

What actually happened was...:

Either:
• The glass bottle becomes a "ghost item" and appears as full on the client until, for example, dropped.
or
• The glass bottle fills up with water but no animation nor sound is played.

Steps to Reproduce:
1. Look just above a water source with a glass bottle in hand
2. Simultaneously right click and quickly swipe down with the mouse
3. The item should now be a ghost water bottle.

The other way around can also be done (looking at the water and swiping up) and the bottle will fill up, albeit with no feedback on the client side.

Edit: As a little more insight, it seems like the bug only occurs when the item uses the onItemRightClick method (aka item's "innate" right click behavior), but it doesn't seem to affect onItemUse/onBlockActivated (aka using the item on a block).
For example, trying to reproduce the bug with a cauldron didn't work, since the cauldron logic works with onBlockActivated. The same applies to block placing, as it happens on onItemUse.