While being tied up by Matthew, Tony is arguing with Jeremiah, who backhands him across the face. But Jeremiah raises his right hand, then the camera angle changes to show him hitting Tony with his left hand.
When Doug is lead out to meet Lincoln his wrist shackles on his right wrist are undone.
When the Time bomb is shown to Tony the hands on the time bomb change several times, when it's carried to the table it reads 12 o'clock, but when it is placed on the table in close up the clock face reads 9.20, Jeremiah moves the clock hands to 12 o'clock, then in long shot the clock face now reads 4 minutes to 12, the clock continues to change between these two settings a number of times.
When the boy David is sent back to 1861 from the time tunnel, the tools that are at his feet disappear from the tunnel but do not materialize in 1861 with him. It is also noteworthy that every time Doug and Tony are transported to a different time they fall and somersault as they land. But the boy materializes in 1861 standing up and under complete control..
Most of John Brown's men had been killed or captured before 1861. The few who remained at large would have been too weakened and demoralized to take part in a high-profile act of terrorism that could easily have led to their capture, especially when war was already almost inevitable.
The Ford's Theater assassination is depicted inaccurately. Only Abraham Lincoln and Mary Todd are depicted as being in the audience at the presidential box, whereas Major Henry Rathbone and Clara Harris were accompanying them in real life. The theater is portrayed as being lit, when it would have been darkened for the performance of Our American Cousin.
At about 15 minutes in, when the train was coming in, modern electrical power lines and transformers on poles could be seen in the background. Being in 1861 these were not yet in service. It was not until after Edison had invented the electric light in 1879 (probably the mid 1890's) that anything like this would be seen.