The Legend of Zelda: Spirit Tracks/Secrets

Pirate Hideout
Go to the cliff on the left and on the end bomb it! You will enter a area with treasure.

Punupia village
The first ocean realm area. Whip on a bird and go south you will see a cliff go across and look around.

Dark ore mine
Go to the right side and do the song of discovery betreen the 2 objects and get treasure.