In 2007 and 2008 Al-Maliki, Prime Minister from 2006 to 2014, used police forces as well as regular and irregular military units to suppress rival Shi’ite factions and to drive Sunni civilians from large parts of Baghdad.

[3] In June 2012 Bogdan took over as commander of Joint Task Force Guantanamo's Detention Group—a position sometimes called the camp's warden—from Colonel Donnie Thomas.

[7] Writing in Time magazine, Ben Fox asserted that an intensive search ordered by Bogdan was one of the triggers for the hunger strike.

"Some detainees resisted with improvised weapons and, in response, four less-than-lethal rounds were fired," according to a statement issued by the prison camps at the U.S. Navy base in Cuba.

Bogdan restricted visiting hours to prior to 4 pm—prior to when many flights arrived on the distant base, while Supermax prisons allowed attorneys access to their clients up until 7 pm.

Bogdan restricted the number of people who could meet with a captive to five, insufficient when defense attorney teams needed the help of paralegals and translators.

Throughout Bogdan's tenure at Guantanamo, human-rights groups including the ACLU and Amnesty International reported that numerous prisoners were innocent and/or were never charged with any crime.

In March 2017 Human Rights Watch reported that, up to that date, 780 individuals had been held at Gitmo yet "731 were released without charges, many after being detained for years.

In September 2019 the student newspaper, the Niner Times, published a lengthy article, "Campus flyer implicates associate vice chancellor of human rights violations during his military service at Guantanamo Bay," detailing Bogdan's controversial career.

UNCC responded by circulating a "Fact Set," a bulleted list containing Chancellor Phil Dubois' responses to the criticisms.

The "Fact Set" stated "the enteral feeding of detainees engaged in hunger strikes has been upheld several times by the courts" and supported other practices employed during Bogdan's tenure at Gitmo, such as the use of rubber bullets and of "groin searches.

"[19] On May 21st, 2024, John Bogdan announced his retirement from the University[20] following several months of pro-Palestinian campus protests at UNC Charlotte, during which the controversy was reignited.