There's one grave that you can go under in Kakariko Village, and when you do, Navi floats off to one side of the room and turns green over some bones lying on the ground. Is this anything special or just some glitch?
If you're talking of the one with all the Keese(bats) then here's what you do:
Kill all the Keese, the door will open, go through the door and keep moving forward to the next room. You will learn the Song of Sun. As for green Navi play Song of Storms and you will see a big fairy.