After you meet Medli by the Dragon Roost Cavern entrance, she asks you to throw her to the top. Do so, and she’ll toss this bottle down to you.
Slightly south of Bomb Island is a submarine. If you’re having trouble finding it, find the man with the telescope on the island, and follow his line of sight. Enter the sub and kill all of the enemies inside to get this prize.
Enter the Shop Ship nearby and shell out a whopping 500 Rupees for this bottle.
After you’ve saved the maidens from the Forsaken Fortress, return to Windfall at night. Talk to Mila, the now-poor girl, and she’ll tell you to go away. Do so, and then she’ll start walking away. You could follow her, and keep your distance so that she can’t see you when she turns around, or you could just wait until she completes her circuit of the island. I prefer to wait, so I’ll tell you where to stand. Between Zunari’s stall and the mansion there’s a gap in the wall that leads to a small dock. Head through the gap and hide along the back side of the building. Now tilt the camera so that you can see through the gap.
Wait a couple of minutes, and she’ll run by the gap. Sneak around the corner to see her in the stall shop, with a thought bubble with a Rupee in it above her head. Walk slowly up behind her, and press A when you’re behind her. Tell her you’re an “Ally of Justice!” then agree to listen to all parts of her sob story, then tell her that you’re not going to just let her go because you’re honest. She’ll see the error of her ways and give you a bottle.