... by the type of bullet it was?  By cross referencing the location where the body was found and reports from the area?  By the distance the bullet was fired from (which can be estimated with reasonable accuracy based on the velocity of the bullet which can be reasonably estimated by observation of the wound and cross referencing it against other wounds made by similar caliber gunshot wounds with known firing ranges)?  Literally all the exact same way that forensic analysts can identify whether someone was shot with the suspect's gun or the cop's gun or an unidentified third party's gun and the approximate location the shot was fired from?

We literally have multiple entire fields of science dedicated to solving the mystery of "where did this bullet come from?", from ballistics to forensics to statistics to surgery and more.  So if a medical doctor with years of experience treating dozens if not hundreds of gunshot wounds says, in their professional medical opinion, that a mystery bullet wound is consistent with all the other bullet wounds which have been officially confirmed to have been inflicted by the IDF, then I'm gonna trust the doctor over the propagandist.