Subtitles correctly describe the bombardment of Fort Sumter by the Confederates as starting the Civil War, but the film depiction shows the reverse. It has the fort firing on the Confederates.
When Lincoln is filling out his ticket for his luggage on the train trip to Washington, the familiar signature of ALincoln, which is familiar to audiences, is in an entirely different writing style that the destination of Washington.
In Ford's theater, Booth entered through a door behind Mary Todd, to the president's right. In reality, he entered through a door to the back left of Lincoln, and fired just below Lincoln's left ear. The movie also shows him jumping from the box through the far left opening (facing the front); once again, he actually jumped through the right opening, directly in front of the president, nicking the corner of Washington's picture with the spur on his ankle, causing him to stumble when he fell, breaking his ankle (albeit, many historians have had theories that he may not have broken it in the jump, he just injured it a bit and because of that he broke it with something involving his horse, later in the night).
General Lee repeatedly addresses an officer as Colonel, or Colonel Marshall, but the officer wears the insignia of a Captain on his collar.
Due to the Blue Laws prevalent at the time, no newspaper in America could publish on Sunday in 1809 (Abraham Lincoln was born on Sunday February 12, 1809).
The US flag is never used as bunting as depicted in the Ford Theater scene.
In both the Union and Confederate parades, the musicians play trombones with forward facing bells. During the Civil War, the bells faced backwards.
Shortly before leaving Mary Todd waiting at the altar (circa 1850), Lincoln opens a drawer and looks at a daguerreotype of his lost love, Ann Rutledge, who had died several years before in 1835. Dagguereotypes did not reach the United States until the mid-1840s.
The gospel song "In the Sweet By and By" is sung in the background when Lincoln is told of his sweetheart's imminent death. The song was not composed until 1867.
While soldiers carry the Lincolns' luggage into the white house, at the upper left corner of the scene, the shadow of a boom mic can be seen - moving the with same speed to the left as the camera does. It can be seen for more than three seconds.