Toward the end of the film, in the establishing shot of John Brown's hanging sequence, three men in formal dress are shown on the left side of the road. Subsequently they appear on the right, and then there is one more.
The film plays fast and loose with historical fact, most noticeably in the other famous officers who are supposed to have graduated West Point with J.E.B. Stuart in 1854: James Longstreet (1842), George Pickett (1846), Philip Sheridan (1853), John Hood (1853), and George Custer (1861).
Just after John Brown is hanged, an Army officer next to the gallows says "So perish all such enemies of the Union." What the officer, Colonel J.T.L.Preston of the Virginia Military Institute said was "So perish all such enemies of Virginia, all such enemies of the Union, all such foes of the human race."
The railroad being built is called the "Santa Fe". The original company was the Atchison and Topeka Railroad Company chartered in 1859. Although one of the original destinations of the railroad, "Santa Fe" was not added to the name of the company until 1863, well after the setting of the movie. Further, contrary to what is shown, initial track laying did not begin until 1868.
The artillery pieces at the Harper's Ferry battle are shown being pulled by teams of four horses. Prior to the Civil War all field artillery pieces, except the M1841 12-pound Gun used teams of six horses (the 12-pound gun required eight horses). A shortage of horses during the War caused field artillery horse teams to be reduced to four horses, a changed which continued after the War.
At the Harper's Ferry battle the troops are shown carrying the Model 1873 (Trapdoor) Carbine, a breech loading weapon which is the standard Hollywood weapon for all U.S. cavalry in the 19th century. The correct weapon would have been the M1854 Rifled Carbine, a muzzle loading weapon. It may also be noted that cavalry was not present at the take over of the Harper's Ferry Arsenal by John Brown.
The final battle takes place in a building called "The Arsenal". The Federal Armory at Harpers Ferry was actually a complex of manufacturing, storage, and office buildings. During the fighting, John Brown's force finally took refuge in the Fire House, one of the smallest of the buildings on the Armory grounds. The Fire House was built of brick but had three large wooden doors through which the firefighting equipment could move.
The goof item below may give away important plot points.
In real life, John Brown said nothing from the gallows. He did, however, hand one of his guards a note on his way to his execution. It read: "I, John Brown, am now quite certain that the crimes of this guilty land will never be purged away but with blood."