After completing the Thunder Dragon Quest, if the player talks to Golo, the Goron outside of the Lanayru Mining Facility entrance, at least twice, Golo tells the player that he is jealous of his discovery. From this point forward, the game becomes impossible to complete and the events at Eldin Volcano and Faron Woods will no longer occur.

Nintendo has since tried to fix this glitch by releasing "The Legend of Zelda: Skyward Sword Save Data Update Channel", a free channel from the Wii Shop.