"To date, a widespread silence and/or confusion has covered up crimes of sexual violence," Stuzinsky wrote. "According to common perception, sexual violence occurred during the regime, but has not been as formally documented as have other atrocities. But failure to punish the perpetrators obviously leads to a climate of general impunity for such crimes."
I would speculate that part of the reason for this lack of documentation is the fact that, even among loyal Khmers Rouge, sexual crimes were taboo. While it might be in keeping with the regime's ethos to torture and kill suspected "enemies," there was no place in "pure" Khmer Rouge ideology for sexual exploitation. If anything, such acts would be associated with the depravity of urban life.
Of course, that doesn't mean sexual crimes didn't happen. But unlike torture and killing of impure elements, they were less likely to be extensively reported and recorded.
According to the recent indictment of torture chief Comrade Duch, "there is evidence of rape being committed at S21, however, recollections differ and it is not clear how many instances occurred."
Duch claims that he was only aware of one such incident, where an interrogator inserted a stick into the genitals of a female prisoner (who happened to be Duch's former schoolteacher). The torture chief claims he reported the violation to his superior, who "did not say anything." The interrogator was then assigned to question a different prisoner.
After this incident, Duch said he suggested wives of Khmer Rouge cadre interrogate female prisoners, a change that was initially implemented. But then, over time, these female interrogators were all eventually arrested, once again leaving men to torture women prisoners.