Be sure to keep an eye on your fairy companion at all times. When Navi turns green and flies over to a spot, it's usually an indication that there is something hidden there. If you don't feel a rumble from the Stone of Agony, then it's most likely a red fairy (refreshes health and magic). Play the Song of Storms or Zelda's Lullaby, to lure it out. In some occasions, Navi also points out potential "scarecrow" spots and hidden caves.