One character says that Mary Surratt should be shown clemency "because of her age and gender". The word "gender", until the very late 20th century, was only a term used in grammar assigning a masculine, feminine or neuter association to a noun. The speaker would certainly have used the word "sex".
When Secretary of State William Seward is stabbed in his bed, the room is shown as being brightly lit. According to historical accounts, though, the room was quite dark, which accounts for Lewis Payne's failure to kill Seward; he missed hitting any vital areas with his knife because he simply could not see his target very well in the dark room. In addition, the elderly Seward was very thin, almost literally 'all skin and bones,' which caused Payne's thrusts to miss their mark.
In the film, President Abraham Lincoln is carried out of the theater and across the street in his full suit, with his shirt neatly in place. According to historical accounts, after Lincoln was shot Dr. Charles Leale and the doctors assisting him in Ford's Theater cut away much of Lincoln's coat and shirt, in a frantic attempt to resuscitate him, before he was moved.
The assassination attempt of William Henry Seward is almost totally incorrect. A servant met Lewis Powell, who was pretending to bring Steward medicine, at the door and tried to stop him from entering. Fred told Powell to come back later because his father was asleep. Fanny, who had dark haired, opened the door to tell Fred that their father was awake. Fred closed the door on her and turned back to Powell, who shot at his head. The gun misfired and he bashed Fred's skull in, leaving a hole and exposing his brain. Powell entered the dark room and shoved Fanny aside as she tried to stop him from attacking Seward. He began stabbing Seward, whose jaw splint deflected the blows somewhat, saving his life. Seward managed to roll off the bed and under it before losing consciousness. Gus and the soldier nurse entered and fought with Powell, who stabbed both about 7 times each before fleeing the scene.
In the film, when Abraham Lincoln is carried into the bedroom of the Peterson Boarding House after being shot, the room is brightly lit. According to all historical accounts, the room was very dark, illuminated by one small gas jet lamp on the wall. In addition, Lincoln is also placed on the bed with his head toward the wall and his feet closest to the doctors. In real life, he was placed with his feet toward the wall and his head closest to the open side of the bed. A historical photograph of the death bed after Lincoln was removed confirms it.
In the scene when the conspirators are being hung, there are men stationed along the top of the wall of the prison. A photograph taken by Alexander Gardner shows twice the amount of men stationed along the top of the wall.
When the Capitol is shown from a distance, the dome appears finished. At the time of of Lincoln's death, large scaffolding surrounded this part of the building. These supports were not removed until January 1866.
During the scene when the conspirators are being hung at the gallows, the camera pans over twice to the photographer positioned on a carriage platform. Only one photographer was allowed in to photograph the hanging: Alexander Gardner. However, he was not on the ground when he took the picture. He set up his camera in an old shoe factory, at a second-story window overlooking the gallows. ("Shooting Lincoln and the Race to Photograph the Story of the Century", Nicholas J.C. Pistor, author)
The goof item below may give away important plot points.
At the hanging, the nooses are placed loosely around the necks of the condemned prisoners, and remain loose until the end. To be effective, the noose must be tightened snugly around the neck to prevent the condemned from slipping out of it when the trap is released.
In the burning Virginia-barn scene shortly before John Wilkes Booth is shot and killed, he is shown wielding what appears to be a single-shot, Sharps .52-caliber 1863-model carbine. Historical accounts -- and even the supposed captured Booth "barn-taken" carbine once on display in a Washington, D.C., museum -- show it to an 1860-model Spencer carbine, a seven-shot, 56/50-caliberr repeater.