Here's every bottle in the game (only 4). I wrote them in chronological order. They are very simple to get. Enjoy!

Dragon Roost Island (F2): Medli gives it to you after throwing her to the dungeon entrance, but before entering the dungeon.
Bomb Island (F5): The bottle is in the submarine in the back of the island. Go in it and defeat every enemy to get to the chest with the bottle.
Rock Spire Isle (B3): Beedle is selling one for 500 rupees. Buy it because there's no other way to get it. Simple.
Windfall Island (D2): You can get this after defeating Helmorac King at the Forsaken Fortress. At night, find Mila, the used-to-be-rich-man's daughter by the auction house. She'll tell you to buzz off. Go to the stairs and she'll run follow her, but becareful! She turns around periodically. Hide around things, like signs, bushes, etc. After getting to Zunari's safe, talk to her. Click every top choice and you get the last bottle.