There are six bottles for Link to collect in Termina. He can use these bottles to solve puzzles, carry fairies and potions and other such things.
Southern Swamp
The first bottle you can find is from Kotatke at the Southern Swamp's Potion Shop. Once you find the witch's missing sister in the nearby woods, return to the Potion Shop and Kotake will give you a bottle that is filled with a Red Potion.
Goron Races
Another bottle can be found once you've defeated Goht in Snowhead Temple. In the Goron races that take place after the boss is defeated, come in first and you will be rewarded with a bottle filled with gold dust.
Romani Ranch
In Romani's Ranch, if you kill all the alien ghosts at 2:30 a.m. on Day 1, Romani will give you a bottle of milk.
Western Ocean
Find the beavers near the western ocean and complete their two part Waterfall Rapids race within the time limit and they will give Link a bottle.
Ikana Graveyard
On Day 3 after 6:00 p.m., go to Ikana Graveyard, wear the Captain's Hat and order the Stalchildren to dig up the grave. Enter the hole, remove your mask, and guide Dampe around so he digs up all the mounds. Defeat the poe that appears to collect this bottle.
Milk Bar
On Day 3 after 6:00 p.m., go to the Milk Bar and deliver Kafei's express mail to his mother, Madame Aroma. She will give you a bottle filled with Chateau Romani.