The slow pace of accountability has infuriated Mr. Mattis, who officials say is dissatisfied with the punishments given largely to junior officers. The reprimands were first reported by The Times after a longer Times investigation into the ambush. The only senior officer to receive a letter of reprimand so far is Maj. Gen. Marcus Hicks, the head of Special Operations forces in Africa, who was already planning to retire.

The delays have led to recriminations within the military’s individual fiefs. Army Gen. Tony Thomas, the leader of Special Operations Command — which includes Green Berets, Navy SEALs and other American commandos around the world — has complained that his troops have been singled out for fault. He has also leveled criticism that Pentagon leaders are protecting United States Africa Command, which oversees missions across the continent.

In a memo to Mr. Mattis on Oct. 1, General Thomas blamed bad relations between Africa Command and the last commander of American commandos in Africa, Brig. Gen. Donald C. Bolduc, as one reason for the failed mission. The memo, obtained by The Times, said the internal tensions had “hindered the ability of commanders, at both levels, to understand, communicate, assess and mitigate risk as events transpired” in October 2017.

Animosity erupted during the video conference at the Pentagon last month between Mr. Mattis; Gen. Mark A. Milley, the Army chief of staff; Mark Esper, the Army secretary; Owen West, the military’s top civilian Special Operations policy official; and Paul C. Ney Jr., the Pentagon general counsel. General Thomas called in from his headquarters at MacDill Air Force Base in Tampa.

Mr. Mattis wasn’t the only one angry, Defense Department officials said. Army officials complained to aides that Mr. Mattis and Marine Gen. Joseph F. Dunford Jr., the chairman of the Joint Chiefs of Staff, had contributed to the morass by allowing Africa Command, whose leader, Gen. Thomas D. Waldhauser, is also a Marine, to essentially investigate itself by appointing General Waldhauser’s own chief of staff, Maj. Gen. Roger L. Cloutier Jr., to conduct the inquiry.

The blowback from the video conference was almost immediate. Maj. Gen. Edwin J. Deedrick Jr., the officer in charge of administering internal punishments, was quickly told by Army leaders to re-examine some of the reprimands from the investigation.

Included in the initial batch of reprimands was one for Captain Perozeni, the leader of the team in Niger that came under attack. Africa Command leaders singled out Captain Perozeni and another junior officer in the early public accounting of the ambush for having “mischaracterized” the mission in a preliminary planning document sent to superiors as a trip to meet with tribal leaders, not a counterterrorism effort.