Creator Killer: Rich Ross was fired from his position as Disney Studios leader weeks after Disney predicted they'd lose $200 million on the project (though currently the actual losses stand at just less than $100 million, and that's if you count the advertising budget). The film, however, hasn't been proven a Stillborn Franchiseyet, though it's dangerously close to being one considering where it stands at the moment.
Executive Meddling: The film was apparently titled John Carter of Mars at first. A promotional logo for the film is a stylized "JCM". But then Mars was dropped, leaving the film with a nondescript title. John Carter is a quite ordinary name compared to the likes of Flash Gordon or Buck Rogers and it stands out precisely because of the association with Mars. No wonder this didn't go over well with fans and others. Not to mention that Mars, including the JCM logo, was downplayed in the marketing (along with any mention of creator Edgar Rice Burroughs, the guy also responsible for Tarzan among others...)
Reportedly, the name change was done to disassociate it with Mars Needs Moms, and/or because people thought girls wouldn't watch movies with "Mars" in the title. Earlier on, the original book title A Princess of Mars was dropped because people thought boys wouldn't watch movies with "princess" in the title (the underperformance of The Princess and the Frog for Disney in 2009 was partially blamed on this).
Old Shame: Andrew Stanton has already confessed that he isn't too satisfied with how the movie turned out.
Troubled Production: There were reservations at Disney about letting Stanton direct the film, despite his obvious sentimental attachment to the material, because he'd never directed a live-action feature before. But, since he'd made WALL-E and Finding Nemo into hits, they let him do it even though he warned them, "I'm not gonna get it right the first time, I'll tell you that right now." Indeed, the film required extensive double reshoots. Throughout production, he ignored the advice of the crewmembers who were live-action veterans in favor of his Pixar friends, back in their offices. Rich Ross and the other studio executives at Disney likewise had little experience with feature films, since most had come from television.
Then, it came time to market the film, which was already handicapped in that department by having no big stars in the cast. A trailer shown at a Disney con did not go over well, and Stanton refused to take any advice from the studio's marketing department. He insisted on using Led Zeppelin's "Kashmir" in the trailer even after it was pointed out to him that a 30-year-old classic-rock song was not likely to resonate with the younger male audience the film was intended for. In addition to all the titling problems noted above.