The Wind Waker Bottles

Go to Bomb Island and sail towards the submarine that Old Man Ho Ho is looking at. Go inside, and defeat the enemies for the bottle.

Head to Beedle's shop over near Rock Spire Isle and purchase it from him for 500 Rupees.

After you save Aryll from the Forsaken Fortress, go to Windfall Island at night (you can use the Song of Passing) and go talk to Mila over by the potion shop, who is now poor due to her father paying her ransom to The Pirates. She will order to leave. Start walking up to Zunari's shop, and you will see a short cutscene of Mila running towards the gate. Wait a few seconds until she stops looking around and continue, and then follow her up to behind the bush to the right of the gate. Wait a few seconds after she is out of sight, as she will still be up on the wooden walkway. Inch on up, so that you can see her, but she can't see you. At this point, she may hear you, and Link will meow to make her think you are just a cat. Continue on up, and she will go into Zunari's shop and try to break into the safe. Sneak up to her and she will turn around, startled. She will ask you several questions, and if you answer them correctly, she will give you a bottle for helping her to realize her mistake. Don't worry if you mess up, because you can always try it again.