Dropping a few Unfortunate Implications examples here, until actual sources can be found for them:
Note that Ben and Arthur (affirmed homosexuals), Victor and the attorney (presumed homosexuals per Mraovich's statements), and the priest (many of whom have been outed as pedophiles in recent years) are killed, while Tammy and Stan (patent heterosexuals) survive, inferring that death is the only fate for sexual deviants, while those who practice approved sexual behaviors will stay alive.
According to Sam Mraovich, the attorney is supposed to be a lesbian. While no doubt an attempt to give homosexual women some token representation in the film, the fact that she's the only character who shows any real sympathy for Ben and Arthur's situation ends up giving the implication that heterosexual people are fundamentally unable to empathize with homosexuals.
After an argument, Ben punches Arthur, knocking the latter down. In the following scene, Ben tends to Arthur's wounds and gives the following gem: "That'll teach you to not say stupid things." An already bad comment is made worse by the following: Considering how irritating Arthur has been up to this point, we actually cheer when Ben throws the punch. This places the audience in an awkward position of tacitly condoning domestic violence, which sadly presides in many hetero- and homosexual relationships and is (usually) condemned.
The tagline for the film is "Only the power of love can defeat a holy soldier on a mission." In the film, however, the opposite happens: Said "holy soldier" actually defeats the ostensibly loving protagonists by killing them. Such success as accomplished by Victor would render the tagline false. With a dose of Fridge Logic, however, one could reinterpret the tagline and the events in the film to imply that the two protagonists lacked the love that was necessary to stop Victor, meaning that Ben and Arthur weren't really in love to begin with. This would give the impression that homosexuals form relationships out of sheer interest (sharing the rent, having a regular sexual partner, proving some point about the viability of a homosexual relationship, etc.) and are simply incapable of (or even uninterested in) committing to steady, trusting relationships based on love.
Dropping a few Unfortunate Implications examples here, until actual sources can be found for them: