Following a plethora of complaints, Nintendo has addressed the game-breaking issue that occurs within the latest Legend of Zelda title, Skyward Sword.
In order to save fans from spoilers, basically at the end of the game you need to revisit three different places in order to get three different things. Get one of these things first and the game will glitch causing you to not be able to proceed. The only solutions Nintendo offered were to either go back to a previous save point and do the process over again, or start the whole game over again from the beginning.
There's no telling when Nintendo will release a patch to cure this issue, but in order to keep it from happening, refer to this statement released on Zelda Informer.
Source: Zelda Informer