The conspirators are shown being kept in a prison located in a barren area miles from Washington. They actually were held in the Old Capitol Prison in the middle of the city (site of the current Supreme Court building).
In the film, President Abraham Lincoln is shown being carried out of the theater and across the street fully dressed, wearing his full suit and shirt neatly in place. In reality, according to historical accounts, Dr. Charles Leale and the doctors assisting him in Ford's Theater moments after Lincoln was shot cut away much of Lincoln's coat and shirt prior to his being moved in a frantic attempt to resuscitate him.
At the hanging, the nooses are placed loosely around the necks of the condemned prisoners and remain so through-out the hanging. To be effective at a hanging, the noose must be tightened snugly around the neck to prevent the prisoner from slipping out of the noose as the trap was released.
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, when Abraham Lincoln is carried into the bedroom of the Peterson Boarding House after being shot, the room is brightly lit; in reality, according to all historical accounts, the room was very dark and dim, being illuminated by only one small gas jet fixture on the wall. In addition, Lincoln is shown in the film being placed on the bed with his head farthest away from the doctors towards the wall and his feet closest to the doctors; in reality, he was placed with his feet towards the wall and his head closest to the open side of the bed, which a historical photograph of the death bed after Lincoln was removed confirms.
Almost the entirety of the assassination attempt of William Henry Seward is incorrect. Lewis Powell, pretending to be bringing medicine, was met at the door by a servant who tried to stop him from entering. Fred, hearing this, also attempted to stop Powell, telling him to come back later because his father was asleep. Fanny (who was dark haired) opened the door to tell Fred that their father was awake. He 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 the brain exposed. He then entered the room and shoved Fanny aside as she tried to stop him from attacking Henry. He began stabbing Henry, the jaw splint deflecting the blows somewhat, saving his life. Henry 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.
As the conspirators are hanged, the two bodies on the right hang much lower than Mary Surratt and the third male on the left. As Mary Surratt was a slender woman, a proficient hangman would have made her rope longer to make sure she'd have enough kinetic energy to snap her neck.