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 an area with treasure.

Papuchia 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.