Image found here
Another glitch has been found! This one appears less common though.
"Reports are trickling in from various discussion boards that there's a game-breaking glitch in Skyward Sword, on the level of the infamous cannon glitch from Twilight Princess. We're not 100% sure what causes the glitch yet, but it involves the non-linear quests in the very last stretch of the . Apparently sometimes, when you complete one of the quests before the other(s), the cutscene triggers needed to finish the other quest(s) get skipped, making it impossible to progress. " - Zelda Informer November 28, 2011
The full article does include a small spoiler aspect, but I read it and it's nothing huge. There aren't any plot points revealed, you just learn the names of some of the quest points that are toward the final stretch of the game. I encourage everyone to read it because it appears that there is a way to be sure to avoid the glitch even though no one is entirely sure what is causing the glitch in the first place. It apparently happens when one thing is done before another thing.
Perhaps that's not explained well, and if that's the case then go and read Zelda Informer's run-down! Save your file from corruption!