Short Eyes depicts a brutal prison environment where homophobia and fear of sexual deviance are pervasive, leading to extreme violence and degradation. The film offers no positive counter-narrative, presenting a bleak and problematic portrayal of themes related to non-normative sexuality and the prejudices surrounding it.

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 Cupcakes, canonically Black in the original play, is portrayed by a Puerto Rican actor in the film adaptation, constituting a race swap.

The film frequently depicts Christian characters as hypocritical, using their faith as a facade for violence, prejudice, or self-interest within the brutal prison environment. The narrative highlights the dissonance between their professed beliefs and their actions, offering no significant counterbalancing positive portrayals.