Nintendo has come out and revealed that at the moment there is a game ending glitch many hours into The Legend of Zelda: Skyward Sword. To be more specific, a certain quest called the “Song of the Hero” can cause a glitch that will completely lock out the rest of the quest and halt all progress in the title forever unless the player has an earlier save.
Nintendo revealed this fact to Zelda Informer and even went about explaining exactly how the glitch could occur and how to avoid it. If the player completes the quest’s desert leg first and speak to a certain Goron not once, but twice, the game locks out completion entirely and halts the game. This can be avoided by not talking to the Goron more than once, or simply perform the desert part of the quest last.