Actors Gal Gadot and Ray Fisher previously claimed Whedon behaved badly towards them on the 2017 superhero movie.
In a lengthy New York magazine article published on Monday, Whedon denied having "threatened" Gadot's career.
"I don't threaten people. Who does that?" said the 57-year-old.
"English is not her first language, and I tend to be annoyingly flowery in my speech," added the film-maker, who took over the reins after original director Zack Snyder withdrew following a family tragedy.
He told the publication the pair argued over a scene that Gadot, who played Wonder Woman in the film, wanted cut.
He said he jokingly told her she would have to tie his body to a railway track and do it over his dead body, and that the Israeli actress had misunderstood that to mean he was threatening to tie her to a track.
But Gadot told New York Magazine there was no such misunderstanding. "I understood perfectly," she told the publication.