Nintendo has admitted that there is a game breaking bug in Zelda: Skyward Sword and that, as of now, there is no fix - all you can do is attempt to avoid the conditions that produce it.
"We have been made aware of the issue that results in being unable to progress in the Song of the Hero quest," Nintendo of America spokesperson Sharon Matheny said in an email to gamers.
"If the game has been saved after completing the sequence of events, it will no longer be possible to proceed through the game on that save file. The only options at that point are to either start the game over or to use an earlier save file to continue."
Fortunately, the bug is relatively difficult to reproduce as a very specific series of events needs to take place for the game break to occur. Nintendo released a how-to guide to break your Skyward Sword game and while it does contain some minor spoilers, if you want to guarantee to avoid this bug, it might be worth while giving it a quick scan.
It all takes place as part of the "Song of the Hero" quest:
1. At the beginning of the quest, go to Lanayru Desert to retrieve the song of the Thunder Dragon.
2. In the Lanayru Mine, speak with Golo the Goron.
3. Complete the Thunder Dragon's event, and receive his song.
4. Before heading to the forest or volcano regions, speak with Golo in the mine again.
5. At this point, the forest and volcano events will no longer occur, making it impossible to continue.
While Matheny said that there was no fix as it stands, she did confirm that Nintendo was taking all feedback for this issue into consideration. There was no announcement of a patch in the works, but a simple recommendation to avoid Golo after you obtain the Thunder Dragon's song.