Found within the game's data are 2 unused tracks from Phantom Hourglass, The Great Sea and Boss Battle themes. Both tracks use different instruments to the originals, along with added echo effects.

In the Japanese version of the game, several direct quotes refer to Tetra being Princess Zelda's grandmother.

There is a full 3D model of the entrance to the Temple of the Ocean King in Spirit Tracks' code. This model, of course, goes entirely unused although you do get to eventually visit the temple via a warp instead of the main entrance.