The autopsy carried out by Coroner Thomas Noguchi showed that Senator Kennedy had been shot three times. One shot entered the head behind the right ear, a second shot near the right armpit and a third roughly one and a half inches below the second. All shots entered the body at a sharply upward angle, moving slightly right to left. These shots are incompatible with eyewitness reports of the shooting. Sirhan had no access to the Senator's rear, and Kennedy never turned more than sideways to Sirhan. In addition, Sirhan fired with his arm parallel to the floor, i.e. straight ahead. Maitre d' Karl Uecker, who had been leading Kennedy forward by the right hand at the time the shooting started, grappled Sirhan after his second shot and pushed the gun away. All these points, as well as the fact that the gun was one and a half to six feet from Kennedy, prove that Sirhan could not have inflicted the fatal wounds to the Senator.

Sirhan's .22 revolver contained eight bullets and he had no chance to reload. This caused a problem for the official version of the assassination as all bullets had been accounted for, except for one which was lost in the ceiling space. Reports indicated that a wooden door jamb contained two bullets. This frame and as many as five or six ceiling tiles were removed from the crime scene for tests. Photographs of the crime scene show at least this many tiles missing and more besides. Los Angeles Police Department criminologist DeWayne Wolfer was quoted as saying "it's unbelievable how many holes there are in the kitchen ceiling." This suggests that LAPD found more bullets (or traces of bullets) than could be accounted for by Sirhan's eight shot revolver, at least seven and probably more.

As well as the problems noted above, there are the reports of suspicious people in the area at the time of the assassination. The first policeman on the scene, Sergeant Paul Schraga, was approached by a couple who told him that they had encountered a young man and woman fleeing the Ambassador Hotel shouting "We shot him! We shot him." When asked who they had shot, the young woman joyously replied, "Senator Kennedy." Schraga sent out an All Points Bulletin on the two suspects. This was the start of the "Polka-dot Dress Girl" controversy. In one of the most intuitive pieces of police deduction since the JFK assassination, LAPD declared that Sirhan was the sole assassin within minutes of the crime. Schraga was asked to cancel his APB, and when he refused, it was canceled by his superiors.

The couple's story was explained by the LAPD as a case of mishearing, stating that the young woman must have said "They shot him!" However, a young woman sitting on a staircase outside the Ambassador Hotel, Sandra Serrano, corroborated the couple's story.

Two witnesses in the pantry also saw armed men, aside from Sirhan and security guard Thane Eugene Cesar. Lisa Urso noticed a blond haired man in a grey suit putting a gun into a holster. A second, unnamed, witness saw a tall, dark-haired man, wearing a black suit, fire two shots and run out of the pantry.