Bug: When magnetic ceilings are found, and you fly towards the ceiling, while in midair, pause and take off the iron boots. You will be able to walk without iron boots.
Bug: If you save while in the cannon room and load the game again, you will be unable to progress any further. The reason for this is that you cannot warp out or leave the room because it says Shad is still in the room with you. But he is not actually there, so it is impossible to ask him to leave, leaving you stuck in the room.
Bug: This is for the Wii version of the game only. In some places, like the Goron Mines and Arbiter's Grounds, there are places where Link can fall into either lava or quicksand. If you do, a short cutscene will play showing Link sinking into the lava/sand. If you press the 'home' button just as Link's fingertips are the only things you can see, you can press the 'Reset' option on the home menu and you will appear on the version of the Bridge of Eldin map you see on the title screen. On this screen, do not press any buttons or the game will freeze. Run to the north where you will find the edge of the map. Run off, and you will get a game over. When the option to retry comes up, hit yes. The scene where King Bulblin kidnaps Colin plays. You will be trapped on the Bridge of Eldin without Epona. Jump off the edge of the bridge three times and retry. The cutscene will play again and you will get to re-play the fight with King Bulblin.
Other mistake: In Kakariko Village, all the signs surrounding Malo Mart (once it opens) claim that it is open 24 hours a day, yet visit after dark and the door is locked.
Continuity mistake: After knocking Ganondorf down the horse in the final battle in Hyrule Castle, his sword is still in his hand. However, when he talks to Link immediately afterwards, it's suddenly in the sheath and he pulls it out.
Continuity mistake: In the cutscene after you first meet Zelda, which is a flashback describing how all the people became spirits, Zelda drops her sword to the ground. However, in the next shot, she is holding it as the camera zooms out.