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Continuity
When agents Anderson and Ward first arrive in town, the air in the street in front of the courthouse is full of dust clouds. When they park and leave their car, the air is clear.
While interrogating Lester in a moving car, the background scenery suddenly indicates that the car is going backward. It's apparent when Lester looks over his shoulder and out the rear window.
While the mayor is being shaved in the barbershop, the barber removes all of the shaving cream, except for his chin. In a subsequent shot, shaving cream is covering the front of his neck.
During the opening chase, the flashing light on the roof of the police car disappears and reappears several times.
When Frank Bailey is trying to escape, Anderson blocks him at the doorway holding up a set of handcuffs with the thumb and forefinger of his left hand. In the next shot, he is dangling the handcuffs from his index finger.
When agents Anderson and Ward first arrive in town, the air in the street in front of the courthouse is full of dust clouds. When they park and leave their car, the air is clear.
Agent Anderson calls Clayton Townley a Grand Dragon of the Klan, usually the leader of a state's Klan chapters. However, Agent Ward said Townley was the Grand Wizard, head of the entire Mississippi White Knights of the Ku Klux Klan.
The film is set in Jessup County, Mississippi. The film is based on incidents that happened in Neshoba County. The producers likely changed the setting to dispel perceptions that the film is a documentary.
Kidnapping the mayor and using intimidation, such as threats of castration, are felonies. Any information obtained by those methods would be inadmissible in court, and would likely destroy the FBI's case. However, the only way anyone else would know is if the mayor said something to someone, and Anderson told Ward he wasn't going to say anything. The mayor knew he would be killed if anybody found out he talked.
When Anderson throws Pell into the chairs at the barbershop, Pell's stunt double has a different hairstyle (balding, with a comb-over).
At around 38:20 in the film, while the sailors and FBI are searching the swamp, an FBI agent jumps into stomach-high water with his service revolver on his hip. This could damage to the gun, rendering it useless and a danger to the agent. No law enforcement agent would jump into water without removing their firearm first.
In one shot during the attempted lynching of Vertis Williams, the noose becomes detached on one side and flops from his neck while he is suspended in the air.
When Rupert and Ward are in the motel room and the shotgun blast occurs, the mirror on the wall cracks a split second before the window and blinds shatter.
Ward and Anderson visit a burned-down church. A tree less than ten feet away has no scorch marks.
The street signs are green with white writing. In the 1960s they would have been white with black writing.
When the agents visit deputy Pell's house in the evening, he is watching baseball on television. In 1964, only afternoon games were televised on Saturday.
When Mrs. Pell is in her living room watching To Tell the Truth (1956), it is dark outside. From 1959 to 1966, the half-hour program aired on CBS at 6:30PM CT, broad daylight during a Mississippi summer.
At the end of the movie, when people are gathered around the tomb marked 1964 and a black woman is singing, a blonde child has ceramic braces, which didn't exist then.
On several occasions, the mayor of the town refers to the sheriff as belonging to "his Sheriff's Department"; however, as a town mayor, he would have had nothing to do with the county police who would answer to a county commissioner (who is never seen). In the real Mississippi Burning incident, there was a clear divide between the Philadelphia town police department and the Neshoba County Sheriff's Department, both of which were complicit in the killings.
When the FBI agents are done driving Lester Cowens around in the back of the car and drop him off in the black part of town, the overhead microphone is clearly reflected in the passenger side of the windshield.
On the ride into Mississippi, Anderson mispronounces the Ku Klux Klan as Klu Klux Klan.