Those people knew entrance from exit wounds.
The autopsy record is admittedly incomplete and shows evidence of tampering. For instance, some X-rays show damage which isn't supported by photographic evidence, and the Assassination Records Review Board found a 90-95% likelihood that two entirely different brains had been examined; brains which provided contradictory evidence as to the damage and the direction of the headshot. What's more, two federal agents who attended the autopsy told the ARRB that the autopsy photos of the back of the head were inaccurate, and that they recalled seeing a large defect in the right rear part of the skull. The agents suggested a flap of scalp was pulled over the right-rear defect before the photos were taken
(
http://ourworld.cs.com/mikegriffith1/id126.htm).
An interesting sidebar: do you know the story of Regis Blahut? He was the CIA liaison to the House Select Committee on Assassinations. In June 1978 Blahut was discovered to have broken into the safe containing the autopsy photos. Blahut's only comment to the press: "There are other things involved that are detrimental to other things."
About Zapruder, it's kinda odd how, when the Warren Commission published stills, the frames showing the fatal head shot were reversed. J Edgar Hoover, whose FBI reviewed the film for the commission, called the reversal "a printing error."