During the scene when Dorothy and Scarecrow are fighting with the trees, Scarecrow says "I'll show you how to get apples" and he gets hit by the apples. The very next scene if you quickly look at Dorothy's shoes, you can see that she is wearing black shoes, not her ruby slippers.

When the stormtroopers break into the control room, the stormtrooper on the right of the screen hits his head on the door frame. On the DVD release they've added a thump when he hits it. THUD! While unintentional, it's still one of the best moments in all the Star Wars films.

In the second half of the film, Frodo has a scar on his lower right cheek, close to his chin. Many times throughout the rest of the film the scar changes position and size on his right cheek. It also appears on his left cheek in flipped shots (most obviously on the slopes of Mount Doom when Sam is cradling his head).