The first one would have to be the docks. Especially when you get onto one of the taxi ships to the different kingdoms. If you are standing in the wrong spot it can glitch and you can be stuck in the air off the ship when its leaving.
Second one I noticed is in the huge mine that has the enterance on the small island. When you try to use a link to go from one place to another in there you can get stuck on the link you emerge at and are immediatly linked back to the other link. So normally it takes u a few tries just to keep going. Usually it takes me 3-9 tries to be able to keep going.