The alleged sexual assault of numerous female trainees by an Army drill sergeant in Missouri has underscored two persistent points of contention in the military: whether the Pentagon has done enough to vet troops who oversee introductory training, and whether men should supervise female trainees at all.

The questions arise anew after the latest set of allegations against a U.S. service member responsible for training subordinate female troops. Army Staff Sgt. Angel M. Sanchez faces a possible court-martial for numerous alleged actions, including forcing recruits to perform oral sex and raping a female soldier while in Afghanistan between March 2011 and March 2012. He appeared at a pretrial hearing on the base that concluded on Wednesday.

The latest allegations come despite a renewed Pentagon effort to crack down on sexual assaults in the military. Since May 2013, the Pentagon has launched more than two dozen initiatives to stop sexual assault; Defense Secretary Chuck Hagel also ordered the services to scrutinize the backgrounds of recruiters, drill instructors, sexual assault response officials and others in positions of authority.

The effort led to the suspension of hundreds of service members, some of whom could be discharged, defense officials said.

In May, the Pentagon said that more than 5,000 sexual assaults had been reported in the military in fiscal 2013, up from 3,374 the year before. The 786-page report lists at least a dozen little-known cases in which authorities investigated allegations that U.S. troops assaulted recruits or trainees they oversaw.

In this Feb, 18, 2011 file photo a vehicle drives out of the Sverdrup Gate of Fort Leonard Wood near Rolla, Mo. Staff Sgt. Angel M. Sanchez, a former drill sergeant at the base, was accused May 28, 2014 at a pretrial hearing at the post of sexually assaulting several female soldiers during the past three years, including at least one while he was deployed in Afghanistan. (Orlin Wagner/AP)

In one incident, a junior enlisted woman in the Air Force reported that she was called into a supply room by a male military training instructor, who fondled her and took off her pants. According to the report, the woman “stated that she froze and [the instructor] had sexual intercourse with her.” The woman reported the incident.

The instructor, whose name and base are not included in the report, was convicted of adultery, obstruction of justice and making a false statement to authorities but acquitted on the more serious charge of aggravated sexual contact, the report said. He was sentenced to 30 months of imprisonment and received a dishonorable discharge.

The incident is among scores of cases that date back decades, some of which erupted into national scandals.

The Air Force, for example, is still dusting itself off after dozens of military training instructors at Lackland Air Force Base in Texas faced court-martial for illegal sexual contact with trainees, including sexual assault and inappropriate consensual sexual relationships. The incidents began in 2009 and came to light in 2011.

The Army also has seen numerous incidents, including previously at Fort Leonard Wood. Between October 2000 and September 2008, 107 drill sergeants were charged with sexual misconduct, leading to 52 courts-martial, the Army Times reported in 2008.

Anu Bhagwati, executive director of the Service Women’s Action Network, which lobbies for equal rights in the military for women, said that if the accusations against Sanchez are true, it shows that the Army’s effort to scrutinize the backgrounds of drill instructors and purge the ranks fell short.

Sanchez became a drill sergeant just last August, after the Pentagon’s house-cleaning attempt was launched. He is now accused of assaulting trainees at Fort Leonard and a female soldier in Afghanistan, and of habitually sexually harassing colleagues in both locations, according to charging documents.

Bhagwati, a former Marine captain, said that’s not a surprise. Units in which sexual harassment is common are prone to sexual assault, she said.

“These guys,” she said of sexual predators, “will continue to abuse and get away with criminal activity unless they’re held accountable within a sophisticated military justice system.”

Sanchez’s attorney, Ernesto Gapasin, said in a phone interview that he has questions about the reliability of some of the women whom Sanchez is accused of assaulting. He continues to serve at Fort Leonard Wood in an office job, said Tiffany Wood, a base spokeswoman.

Lt. Col. Cathy Wilkinson, a Pentagon spokeswoman, said it is unlikely the Defense Department will push for a widespread changes in which female military instructors train female recruits, something the Marine Corps has done for decades. In fact, the opposite appears to be true: Army Gen. Martin E. Dempsey, chairman of the Joint Chiefs, has said he believes integrating women into more assignments could curb sexual assault.

“When you have one part of the population that is designated as warriors and another part that’s designated as something else, I think that disparity begins to establish a psychology that in some cases, it led to that environment,” Dempsey said last year.

Retired Army Maj. Gen. Robert D. Shadley, who was in charge of Aberdeen Proving Ground in Maryland when a similar sexual assault scandal erupted there in 1996, said he does not think the military’s sexual assault problems require wholesale changes, or for the military to require men and women to be trained separately.

As in more recent cases, the crisis at Aberdeen involved drill sergeants using their positions to push women into sex and keep quiet about it afterward. At least four male soldiers were later sentenced to prison time.

Shadley, who received a reprimand from the Army for not discovering the problems quickly enough, said the military still needs to treat sexual assault as a “force protection problem” that requires the same kind of constant attention as looking for explosives in Afghanistan.

“You just can’t say we’re going to train everyone up and it will be okay,” he said. “Every day is a new fight.”