Numerous continuity errors involving the percussion locks on the firearms. Rifles and pistols go from uncocked to half-cocked to fully cocked and back to uncocked, then are shown being cocked by the character.
The sergeant that drops into the trench that Newt and his nephew are hiding in orders everybody to "fix bayonets". Before this order and just in shot, you will see that he has no bayonet fixed then when the scene cuts back to him he does then after another scene switch comes back to him the bayonet is gone again.
When the supposed Confederate Flag is taken down, to be replaced with the Stars and Stripes, the wrong flag is used. The flag being taken down was actually the battle standard of the Army of Northern Virginia. It should have been the "The Stainless Banner".
During the montage sequence of photos of the fall of Vicksburg, one of the photos shows the Dunker Church, which was the Battle of Antietam in September 1862.
When they hook the flag on the rope to raise it up up the flag pole, it is hooked with a snap hook, which was not patented until 1890.
A majority of the movie is filmed in the swamps. But we never see any of the people living there being bothered by mosquitoes, even by night.
In the camp scene of July 1863, someone with a harmonica is playing "Beautiful Dreamer" by Stephen Foster. It was published posthumously in March 1864, by Wm. A. Pond & Co. of New York.
However, the song's copyright date is 1862. It was written then, or possibly earlier. It is possible (albeit unlikely) that the song had been performed and heard before 1864.
Newt is shown waving his cap. Later, a close-up reveals no bullet holes in the cap, but it was never implied, stated, or shown that the cap was ever actually shot.
When the Confederates are surveying the damage after the arson, one of them is wearing a U.S. Army hat.
When the plantation owner comes back home after the war and walks through the front door, a thermostat is visible on the wall to his left.
When Newton Knight and his young cousin Daniel are sheltering in a rifle pit during a battle, a prominent Phillips head screw can be seen holding the parapet of the rifle pit together. The Phillips head screw wasn't invented until the 1930s.
When Newton's wife finds him, she says that she and the son walked from Birmingham. Birmingham, Alabama was not established until 1871.
Hood says "Calvary can't get into those swamps." He means 'cavalry'. To be fair, this is a common error, then and now, so his character might well have spoken like that.