A black and white shot of "Air Force One" departing is not the actual aircraft. Aircraft 26000 had a large presidential seal on both sides of the fuselage forward of the leading edge of the wing. The aircraft shown in the shot lacks the seal.
In the movie, the Hertz sign atop the Texas School Book Depository building shows FORDS in the panel under the clock. Back in 1963 when the assassination occurred, this panel read CHEVROLETS.
In a aerial establishing shot of Dallas for the week before the assassination in 1963, JFK's cenotaph memorial (built in 1968) can clearly be seen.
A post 1963 VW Bug and Chevy Van are in the scene where Oswald is escaping from the School Book Depository.