"We had an air-gapped computer that just had its [firmware] BIOS reflashed, a fresh disk drive installed, and zero data on it, installed from a Windows system CD," Ruiu said. "At one point, we were editing some of the components and our registry editor got disabled. It was like: wait a minute, how can that happen? How can the machine react and attack the software that we're using to attack it? This is an air-gapped machine and all of a sudden the search function in the registry editor stopped working when we were using it to search for their keys."

"Ruiu posited another theory that sounds like something from the screenplay of a post-apocalyptic movie: "badBIOS," as Ruiu dubbed the malware, has the ability to use high-frequency transmissions passed between computer speakers and microphones to bridge airgaps."

I presume the computer that had reflashed BIOS, fresh disk drive, with zero data, installed from a Windows System CD, was uninfected. Then it became infected. Then he mentions a theory that it jumps airgaps with speakers and microphones.

This strongly implies that the claim is of a virus that jumps airgaps from an uninfected machine to an infected one through sound.

Which part of this is incorrect?

(Also, the claim that infected computers communicate via sound to bridge airgaps is not mutually exclusive with the claim that infection can spread over airgaps. So what you quoted does not contradict this claim, which is why I didn't take it as a refutation of my previous reading).