The positions of the unconscious Yankee soldiers changes between shots.
The second to last button on Cyrus' confederate uniform is undone once he is dressed, but is buttoned in the next shot.
When Homer (actually Buster Keaton's stunt double) falls off the unicycle, he accidentally kicks Monte Collins in the face.
When Zeb Montague is first introduced in the Yankees' headquarters office, he does not have a mustache or sideburns, as his character is supposed to.