When the Chosen One talks to his friends while they're wounded in the field, he has a tattoo saying "Mouth" with an arrow on his right cheek. The tattoo is given to him by an old man in a deleted torture scene, and can't be seen in any other scenes in the film.
When Master Pain first appears in town to demonstrate his skill, he is wearing his robe while following the mayor. In the next shot, he doesn't have the robe on (a shot where he rips it off was filmed, but omitted).
When the infant Chosen One is rolling down a hill, his shoe falls off. In the next shot, he has both of them on again. Shortly thereafter, he loses the same shoe a second time (exact same footage), and then both of them reappear on his feet. Some other segments are shown 3 or 4 times.
During the final fight when the song "Black Betty" is first played and the Chosen One starts dancing, there's a shot of Master Pain being played by Leo Lee, the actor who plays Young Master Pain instead of Fei Lung, the primary Master Pain actor.