Hmm... There are four bottles and they can be found at these locations.

1. Bought at the village in Hyrule lightworld from a vendor.
2. Found in the back of the bar in Hyrule village in the lightworld.
3. Found underneath the bridge just east of Link's House
4. Found just outside the desert in the lightworld.

To get the fourth, and I believe to be most difficult bottle, go to where the weapon smith's house would be in Hyrule Village in the darkworld. There should be an unopenable chest there later on in the game. Bring the chest to the guy standing next to the sign that say's "Don't bother the man standing next to the sign..." and talk to him while the locked chest with the key inside it is with you.

*Hint* Don't use your Pegasus boots or you will leave the chest behind you.

Good luck saving Hyrule from Agnim!