Numerous doubts have been raised over Peltier's guilt and the fairness of his trial, based on allegations and inconsistencies regarding the FBI and prosecution's handling of this case:

    FBI radio intercepts indicated that the two FBI agents had been pursuing a red pickup truck; this was confirmed by the FBI the day after the shootout. Red pickup trucks near the reservation were stopped for weeks, but Leonard Peltier did not drive a red pickup truck. Evidence was given that Peltier was driving a suburban vehicle, sometimes known as a stationwagon or panelvan, a large sedan with an enclosed rear section, able to be accessed from inside the front of the vehicle, by climbing over the seats, or by opening the door or hatch at the rear. Peltier's vehicle was red with a white roof; not a red, open-tray pickup truck with no white paint. The FBI agents' radio message said that the suspect they were pursuing was driving a red pickup truck, with no additional details. At Peltier's trial, the FBI testified that it had been searching for a red and white van, which Peltier was sometimes seen driving. This was a highly contentious matter of evidence in the trials.

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    Unlike the juries in similar prosecutions against AIM leaders at the time, the Fargo jury were not allowed to hear about other cases in which the FBI had been rebuked for tampering with evidence and witnesses.

    An FBI ballistics expert testimony during the trial asserted that a shell case found near the dead agents' bodies matched the rifle tied to Peltier. He said that a forensics test of the firing pin, which would have more definitively matched the gun to the cartridge case, was not performed because the gun was damaged in the fire. A less definitive test indicated that the extractor marks on the case and rifle matched.

    Years later, after an FOIA request, the FBI ballistics expert's records were examined. His report said that he had performed a ballistics test of the firing pin and concluded that the cartridge case from the scene of the crime did not come from the rifle tied to Peltier. That evidence was withheld from the jury during the trial

Source: as above

Though the FBI's investigation indicated that an AR-15 was used to kill the agents, several different AR-15s were in the area at the time of the shootout. Also, no other cartridge cases or evidence about them were offered by the prosecutor's office, although other bullets were fired at the crime scene. During the trial, all the bullets and bullet fragments found at the scene were provided as evidence and detailed by Cortland Cunningham, FBI Firearms expert, in testimony.

(Ref US v Leonard Peltier Vol 9).

At the conclusion of Peltier's trial, the prosecutor closed his argument saying, "We proved that he went down to the bodies and executed those two young men at point blank range." However, at the appellate hearing, the government attorney conceded, "We had a murder. We had numerous shooters. We do not know who specifically fired what killing shots...We do not know who shot the agents

(Ref US v Leonard Peltier Vol 9).

The Pennsylvania Parole Commission, which presides over the Lewisburg prison where Peltier was held, denied Peltier parole in 1993 based on their finding that he "participated in the premeditated and cold blooded execution of those two officers." But, the Parole Commission has since stated that it "recognizes that the prosecution has conceded the lack of any direct evidence that [Peltier] personally participated in the executions of the two FBI agents

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