The 32-year-old action star is taking a stance against sexual harassment - producer Ratner has been accused of multiple instances of misconduct.
Gadot is said to be refusing to let a series celebrating women's empowerment benefit a man accused of harassing women.
"She's tough, stands by her principles [and] knows the best way to hit people like Brett Ratner is in the wallet," a source told Page Six.
"She also knows that Warner Bros has to side with her on this issue as it develops. They can't have a movie rooted in women's empowerment being part-financed by a man accused of sexual misconduct against women."
Wonder Woman, directed by Patty Jenkins, is one of 2017's biggest box office success stories with a US$822 million worldwide haul. It was seen as a breakthrough for Hollywood, in which few women direct or have the lead role in such big-budget studio projects.
Warner Bros wants both Jenkins and Gadot back for the sequel, but has a co-financing deal with Ratner's RatPac-Dune Entertainment that will end in 2018.
Ratner is facing sexual harassment allegations from several women, including Olivia Munn and Ellen Page.
Gadot has not accused the 48-year-old movie mogul of harassment herself, but is taking a stand with the women who have.
Ratner, through his lawyer, has denied the allegations.