In December, 2004, questions about the scientific evidence in the Willingham case began to surface. Maurice Possley and Steve Mills, of the Chicago Tribune, had published an investigative series on flaws in forensic science; upon learning of Hurst's report, Possley and Mills asked three fire experts, including John Lentini, to examine the original investigation. The experts concurred with Hurst's report. Nearly two years later, the Innocence Project commissioned Lentini and three other top fire investigators to conduct an independent review of the arson evidence in the Willingham case. The panel concluded that "each and every one" of the indicators of arson had been "scientifically proven to be invalid."
In 2005, Texas established a government commission to investigate allegations of error and misconduct by forensic scientists. The first cases that are being reviewed by the commission are those of Willingham and Willis. In mid-August, the noted fire scientist Craig Beyler, who was hired by the commission, completed his investigation. In a scathing report, he concluded that investigators in the Willingham case had no scientific basis for claiming that the fire was arson, ignored evidence that contradicted their theory, had no comprehension of flashover and fire dynamics, relied on discredited folklore, and failed to eliminate potential accidental or alternative causes of the fire. He said that Vasquez's approach seemed to deny "rational reasoning" and was more "characteristic of mystics or psychics."