The film portrays same-sex interactions almost exclusively through the lens of prison violence, power dynamics, and sexual assault. Characters perceived as effeminate are targeted for abuse, and queer identity is largely associated with vulnerability, degradation, and misery. There is no counterbalancing positive or neutral depiction.

The film 'Short Eyes' features 'Cupcakes,' a gender non-conforming character, who is consistently depicted as a victim of severe verbal and physical abuse, including sexual assault, by other inmates. The portrayal emphasizes degradation and vulnerability within the brutal prison environment, presenting the character's identity primarily as a source of misery and mockery without affirming their worth or complexity.

The character Pimp, widely established as Black in the original play and its context, is portrayed by Shawn Elliott, an actor of Puerto Rican descent, constituting a race swap for a significant character.

The film portrays Christianity negatively through the character of Mr. Nettles, a devout Christian accused of child molestation. His piety is depicted as a hypocritical facade, failing to offer genuine redemption or moral guidance in the brutal prison environment. The narrative uses this character to highlight the dark side of human nature and the potential for religious belief to be a source of self-deception rather than virtue.