3) Scientists in the film thought they were being interviewed for a different movie.
As Richard Dawkins, PZ Myers, Eugenie Scott, Michael Shermer and other proponents of evolution appearing in Expelled have publicly remarked, the producers first arranged to interview them for a film that was to be called Crossroads, which was allegedly a documentary on "the intersection of science and religion." They were subsequently surprised to learn that they were appearing in Expelled, which "exposes the widespread persecution of scientists and educators who are pursuing legitimate, opposing scientific views to the reigning orthodoxy," to quote from the film's press kit.

When exactly did Crossroads become Expelled? The producers have said that the shift in the film's title and message occurred after the interviews with the scientists, as the accumulating evidence gradually persuaded them that ID believers were oppressed. Yet as blogger Wesley Elsberry discovered when he searched domain registrations, the producers registered the URL "expelledthemovie.com" on March 1, 2007—more than a month (and in some cases, several months) before the scientists were interviewed. The producers never registered the URL "crossroadsthemovie.com". Those facts raise doubt that Crossroads was still the working title for the movie when the scientists were interviewed.

4) The ID-sympathetic researcher whom the film paints as having lost his job at the Smithsonian Institution was never an employee there.
One section of Expelled relates the case of Richard Sternberg, who was a researcher at the Smithsonian Institution's National Museum of Natural History and editor of the journal Proceedings of the Biological Society of Washington. According to the film, after Sternberg approved the publication of a pro-ID paper by Stephen C. Meyer of the Discovery Institute, he lost his editorship, was demoted at the Smithsonian, was moved to a more remote office, and suffered other professional setbacks. The film mentions a 2006 House Committee on Oversight and Government Reform report prepared for Rep. Mark Souder (R–Ind.), "Intolerance and the Politicization of Science at the Smithsonian," that denounced Sternberg's mistreatment.

This selective retelling of the Sternberg affair omits details that are awkward for the movie's case, however. Sternberg was never an employee of the Smithsonian: his term as a research associate always had a limited duration, and when it ended he was offered a new position as a research collaborator. As editor, Sternberg's decision to "peer-review" and approve Meyer's paper by himself was highly questionable on several grounds, which was why the scientific society that published the journal later repudiated it. Sternberg had always been planning to step down as the journal's editor—the issue in which he published the paper was already scheduled to be his last.

The report prepared by Rep. Souder, who had previously expressed pro-ID views, was never officially accepted into the Congressional Record. Notwithstanding the report's conclusions, its appendix contains copies of e-mails and other documents in which Sternberg's superiors and others specifically argued against penalizing him for his ID views. (More detailed descriptions of the Sternberg case can be found on Ed Brayton's blog Dispatches from the Culture Wars and on Wikipedia.)