As the movie progresses, Todd reveals his ability to act with the same ruthless cruelty that Dussander did in the concentration camp. Thus, he completes the murder of a homeless man that Dussander initiated, and he efficiently disposes of the corpse and the man's effects.

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Increasingly focused on listening to Dussander's accounts, he ignores many other aspects of his life. His grades plummet, and he no longer excels at sports. When his friends realize that he has lost interest in girls, they challenge him to have sex with the easily available Becky Trask (Heather McComb). However, Todd is unable to get an erection, and Becky loudly mocks him as a homosexual.

In an interview with Eddie Cockrell at the 1998 Toronto Film Festival, Singer insisted that he had not wanted to suggest any erotic dimensions in the relationship between Todd and Dussander: "I never intended any between the two characters, but there is a smattering of that with the guidance counselor [David Schwimmer] and the homeless guy [Elias Koteas], which can be kind of interesting." Furthermore, in response to Cockrell's question about whether he had encouraged McKellan to "play the character with potentially gay overtones," Singer asserted, "No, not at all, I don't think so, no. In fact he played it very straight."

Yet, as Caroline McKahan, Jason Picart, and others have noted, the exceptional emotional intensity of the interactions between the two lead characters in Dussander's claustrophobic home evokes sexual tension, whether intended by Singer or not. Dussander makes the erotic dimension of their relationship explicit when he tells Todd, "Don't you see? We are fucking each other."

The fervor of their involvement is emphasized by shifting close-ups of their eyes and by John Ottman's soaring, romantic score. Also contributing to the erotic dimensions of the film are soft, golden lighting; flattering camera angles; and other devices that emphasize Brad Renfro's youthful beauty.

As The Usual Suspects does, Apt Pupil reveals the ambiguous interactions of homoeroticism, homophobia, and violence. In the shower of the high school gym, Todd imagines that the youths surrounding him are transformed into elderly men in a concentration camp. Although the men are haggard and deformed by suffering, they and Todd exchange intense, desiring glances. Furthermore, in a provocative montage, Singer superimposes photographs of Holocaust victims over the barely clad Todd, as he twists and turns in his sleep.

As Singer acknowledged in the interview with Cockrell, homosexuality also is suggested in the incidents involving the homeless man and the guidance counselor. Wearing a woman's scarf and displaying effeminate gestures, the homeless man is characterized as stereotypically gay. On the night that Dussander invites him into his house, the two are shown on a bus, intently gazing at one another in a way that evokes cruising. Moreover, Dussander tenderly caresses the man's neck before he stabs him.

It is easy to imagine that Edward French, the kindly high school counselor played by Schwimmer, is gay. In any case, French immediately succumbs to Todd's threat to accuse him of sexual molestation if he reveals Todd's involvement with Dussander (whose Nazi past has become publicly known by this point in the movie). This incident provides an eerie precedent for the smear campaign against Singer and his associates.

The accusations made against Singer and others involved in the production concerned the filming of the crucial shower scene on April 2, 1997. Originally, Singer and his assistants tried to film the youths showering with g-strings. However, the extras were asked to remove the g-strings because they remained highly visible in the rear views of their bodies.

Among the approximately thirty extras involved in the shower scene, six youths later claimed that they had been psychologically intimidated and that they had been filmed naked against their will. They further insisted that they had been sexually ogled and otherwise humiliated during the filming process. Within two weeks, the parents of the six youths filed a total of five criminal suits against Singer, Phoenix Pictures, and other individuals and corporations involved in the production of Apt Pupil.