They got pissy that the show made tranny jokes in one episode (complete with a lizard creature that turns human being repulsed when Mulder explained transgender people to him), an episode which featured Islamic terrorists as the bad guys (complete with a version of events where the Islamic terrorists actually MURDERED PEOPLE at a "draw obscene pictures of Mohammed" event and the plot twist that a group of Muslim immigrants brought into the community by a SJW church group WERE terrorists and were building bombs to kill more innocent people).
Then there was Joel McHale of Community/The Soup fame as an Alex Jones/Glenn Beck type who was right all along, on everything he ranted about and the fact that Scully was overtly sexually attracted to him. And Scully pushing what they felt was an "anti-vaxxer" agenda when she brought up the plot point of the Syndicate using smallpox vaccines as a cover for illegal medical experiments on the public, as well as the Cigarette Smoking Man justifying his move to end the world in the final episode via "Global Warming" just like Samuel L Jackson did in the film Kingsmen.
>>317665
It's more that the second X-Files film had homophobic elements to it that helped doom it with the fanbase (though in the film's defense, the homophobia just exhibit A for why the second X-Files film sucked) and that poisoned the well. Also, there is the "you can't do a conspiracy sci-fi show during a Democrat Presidency" garbage that SJW have (which killed the revival of V), and a lot of people, most notably MovieBob but others as well, basically saying Mulder was too "problematic" to work in any sort of modern version of the X-Files because Mulder is a conspiracy theory type and SJW believe you can only be a conspiracy theory type and allowed to function in polite society, during a time Republicans control the White House.
There have been public calls ranging from "the tenth season never happened!" discontinuity and those who want Chris Carter FIRED from his own show and replaced with a SJW friendly showrunner, with SJW types flat out EVOKING George Lucas as far as saying that Carter should be told to fuck off and replaced with Bryan Fuller or Vince Gilligan.