Military commissions' rules allow for important legal issues occurring during the trial to be decided by the executive branch official who brought the charges against the accused. Important legal questions raised by the defence counsel regarding matters such as the jurisdiction of the commission, evidentiary rulings or the elements of the crime are decided by the very same executive officer who initiated the charges and approved the prosecution. This is clearly violative of the principle of separation of judicial and prosecutorial roles recognized by all civilized nations of the world.

Military commissions violate established rules of international humanitarian law (IHL) - a subset of international law that applies only in times of armed conflict. Briefly, IHL confers protection and assistance on the wounded and sick, details treatment of prisoners of war and lists the lawful and unlawful methods and means of warfare. The purpose of IHL is to mitigate suffering and to afford a delicate compromise between humanity and necessity in times of war. Geneva Conventions of 1949 are one of the major instruments of IHL.

One of the biggest flaws in military commissions is that they blur the distinction between the two categories recognized under IHL: combatants and civilians. IHL allows the creation of creation of military commissions within the context of armed conflict. However, IHL does not allow prosecution of civilians before military commissions. The Guantanamo Bay military commissions, on the other hand, are designed to prosecute civilians who had a remote connection or no connection with an armed conflict.

The definition of the term armed conflict is so broadly coined under the rules of the military commissions that virtually any person anywhere in the world could be tried before them. It is mentioned that the defendant's conduct need only be distantly or vaguely related to a traditional armed conflict. The nexus between the defendant and the armed conflict "...could involve, but is not limited to, time, location, or purpose of the conduct in relation to the armed hostilities...This element does not require a declaration of war, ongoing mutual hostilities, or confrontation involving a regular national armed force." In short, under the jurisdiction of military commissions includes acts that are normally considered civilian crimes and lack the required nexus with armed conflict.

Military commissions are also incompatible with Third Geneva Convention relative to the treatment of prisoners of war (POWs). There have been instances of improper determination of the status of captured persons who took part in hostilities. While it may be possible legal to deny POW status to members of al-Qaeda who fail to satisfy the criterion required for enjoying POW status. It is argued that the same status should never have been denied to Taliban combatants who formed part of the armed forces of Afghanistan. Detained Taliban combatants should consequently have been designated as POWs under the Third Geneva Convention.