Annabelle gets drenched when she and Johnnie stop for water, but as they return to the engine, her dress is dry.
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.
When Johnnie is chopping wood on the train, the piece of wood changes size between the different shots.
When the General is first stolen, Johnnie 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.
When Johnnie is chasing the General in the Texas, during most of the chase the engine has a sliding hatch in the cab roof. Just before Johnnie abandons the Texas, the roof changes to a smooth roof without a hatch and slightly different shape.
The Union General that Johnny takes prisoner is wearing the rank of Lieutenant General (3 stars) on his shoulders. At the time the highest in the Union Army was Major General. Only George Washington had held the rank of Lieutenant General. This changed U. S. Grant was promoted to Lieutenant General.
The cowcatchers on Western & Atlantic RR trains had horizontal bars, rather than the vertical ones seen on all three trains in the film.
When Johnnie gets switched on the siding and reverses back onto the mainline, his locomotive slides a fair distance after the drivers stop. This likely indicates that the rails had been heavily greased to prepare for the wheel slip scene following it.
When Johnnie 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.
The enlistment scene takes place in 1861 but the "Southern Cross" flag hanging outside the enlistment office wasn't used until 1862.
The General is equipped with air brakes which weren't invented until 1872 by George Westinghouse.
The General and Texas are seen numbered 3 and 5, respectively. At the time the film is set, the engines of the Western and Atlantic were only known by their names, as were the General and the Texas. The railroads in the Confederacy did not begin numbering their engines until after the war. At that time, the General and Texas were numbered 39 and 49, respectively. The General did not receive the number 3 until the 1880s, and the Texas was renumbered 12 in 1880, then 212 in 1890, and never received the number 5.
The pistol Johnnie uses near the end of the film to arrest the Yankee officer in the cab of the General is a Colt revolver from the 1870s.
The Union soldier killed by the flying sword blade uses a Springfield trapdoor rifle, which was not available during the Civil War.