In the film's trailer, Cumberbatch's character is asked by Zoolander, played by Ben Stiller, whether they're a "male model or female model" to which Cumberbatch replies "All is All".
Hansel, Owen Wilson, then jokes "I think what he's asking is do you have a hotdog or a bun?"
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A petition against the film claimed "by hiring a cis actor to play a non-binary individual in a clearly negative way, they (sic) film endorses harmful and dangerous perceptions of the queer community at large."
Theroux, who is married to actress Jennifer Aniston, said he never aimed to offend anyone and was critical of those that took to social media to attack the film.
"With social media and and all the rest of it, people's issues need to be heard... at the end of the day people are looking for bandwidth. People are looking to inject their voice," he said.
"But our target is not, and never was, to disenfranchise anyone."
Zoolander 2 premieres in New Zealand on Thursday, February 11.
-AAP