Continuity: When the General is first stolen, Johnny is washing his hands; when he sees the train pulling away, he walks away from the sink with his hands covered in soap, but in the following reverse shot where he tells the passengers what has happened, his hands are clean.
Anachronisms: The enlistment scene takes place in 1861 but the "Southern Cross" flag hanging outside the enlistment office wasn't used until 1862.
Anachronisms: The movie takes place during the Civil War in the 1860s. However the General is equipped with air brakes which weren't invented until 1872 by George Westinghouse.
Anachronisms: The Union infantryman, who was killed by the flying sword blade, was using a Springfield trapdoor rifle which was not made until after the end of the Civil War.
Continuity: When Johnny is chopping wood on the train, the piece of wood changes size between the different shots.
Continuity: Johnny's and Annabelle's clothes are dry, neat, and clean the morning after camping outside without shelter during the thunderstorm
Revealing mistakes: When Johnny is running through the woods to escape the Union soldiers, his hat drops from the tree before his head hits the hat to dislodge it.
Continuity: When Annabelle Lee is brought inside the Union headquarters by two soldiers, her clothes are soaking wet from the rain clearly visible through a window, but the soldiers' clothes are dry.
Continuity: When Keaton is chasing the General in the Texas, during most of the chase the engine has a sliding hatch in the cab roof, but just before Keaton abandons the Texas, the roof changes to a smooth roof without a hatch, and slightly different shape, obviously meaning he changed engines.