Toward the end of the series, Charles Main's rank switches back and forth between Captain and Major in various scenes (insignia is not consistent).
At Appomattox General Lee is depicted as wearing the rank insignia of a colonel, which he did for most of the war. In reality General Lee wore a new uniform at Appomattox that displayed the wreathed stars of a general officer.
In the show General George Armstrong Custer is depicted as entering the McLean House among the other Federal general officers present for the surrender. In reality, however, General Custer was absent this meeting.