Ronald Bailey at Reason magazine has reviewed "Expelled," and is one of the few who has pointed out that:
Yet despite its topic, the film is entirely free of scientific content--no scientific evidence against biological evolution and none for "intelligent design" (ID) theory is given. Which makes sense because biological evolution is amply supported by evidence from the fossil record, molecular biology, and morphology. For example, the younger the rocks in which fossils are found, the more closely they resemble species alive today, and the older the rocks, the less resemblance there is. In addition, molecular biology confirms that the more distantly related the fossil record suggests species lineages are, the more their genes differ."Expelled" is standard creationist and ID fare, in that regard.
Instead of evaluating this evidence, Stein spends most of the movie asking various proponents of evolutionary theory, including Richard Dawkins, P.Z. Myers, Michael Ruse, and Daniel Dennett, for their religious views. Neither the producers nor Stein understand that offering critiques of a theory with which they disagree is not the same as proving their own theory.