Well, to be accurate, over at his blog, Darwin's God, Cornelius Hunter wrote:
In his book The Making of the Fittest, Sean Carroll writes “the degree of similarity in DNA is an index of the [evolutionary] relatedness of species.”  This can only make sense if we first assume evolution is true. But Carroll's book is a defense of evolution, intended to demonstrate that the theory is true without first assuming it is true. He seeks to prove evolution is true, but he begins with evolutionary reasoning and interpretations. That is circular reasoning. Unfortunately such circular reasoning is a common motif in the evolution genre.
So he really didn't come out and accuse Behe of circular reasoning. However, since Behe uses the same reasoning* to arrive at the same conclusion that Sean Carroll arrived at, then by a simple use of non-circular reasoning we can conclude that Cornelius Hunter has accused Michael Behe of using circular reasoning.
Frankly, I don't really care if Carroll or Behe has used circular reasoning. I don't really care if common descent is true or false. I think it is, but so what? I've been wrong about many things. What I care about is why Hunter has no problem accusing Carroll of using circular reasoning, but wouldn't for the life of him ever accuse Behe of using circular reasoning.
Does this have anything to do with Intelligent Design? I don't know. Behe says it doesn't, but he devoted seven pages of The Edge of Evolution to defending common descent, using the supposed circular reasoning that is a "common motif in the evolution genre."
Cornelius Hunter may or may not think this has something to do with Intelligent Design. He certainly thinks it is worthy of attack.
All I want to know is why doesn't he attack Behe. I have my suspicions. But they involve things such as subterfuge and duplicity. And I get depressed when I start thinking about that stuff.
* Somebody has screwed around with the URL. I guess they don't want people to know the content of Behe's argument. So I'll reprint what I wrote in that thread:
More compelling evidence for the shared ancestry of humans and other primates comes from their hemoglobin — not just their working hemoglobin, but a broken hemoglobin gene, too.  In one region of our genomes humans have five genes for proteins that act at various stages of development (from embryo through adult) as the second (betalike) chain of hemoglobin. This includes the gene for the beta chain itself, two almost identical copies of a gamma chain (which occurs in fetal hemoglobin), and several others. Chimpanzees have the very same genes in the very same order. In the region between the two gamma genes and a gene that works after birth, human DNA contains a broken gene (called a "pseudogene") that closely resembles a working gene for a beta chain, but has features in its sequence that preclude it from coding successfully for a protein.
"Chimp DNA has a very similar pseudogene at the same position. The beginning of the human pseudogene has two particular changes in two nucleotide letters that seems to deactivate the gene. The chimp pseudogene has the exact same changes. A bit further down in the human pseudogene is a deletion mutation, where one particular letter is missing. For technical reasons, the deletion irrevocably messes up the gene's coding. The very same letter is missing in the chimp gene. Toward the end of the human pseudogene another letter is missing. The chimp pseudogene is missing it, too.
"The same mistakes in the same gene in the same positions of both human and chimp DNA. If a common ancestor first sustained the mutational mistakes and subsequently gave rise to those two modern species, that would very readily account for why both species have them now. It's hard to imagine how there could be stronger evidence for common ancestry of chimps and humans.
"That strong evidence from the pseudogene points well beyond the ancestry of humans. Despite some remaining puzzles,  there's no reason to doubt that Darwin had this point right, that all creatures on earth are biological relatives." (p. 71-72)
 Chang, L.Y., and Slightom, J.L 1984. Isolation and nucleotide sequence analysis of the beta-type globin pseudogene from human, gorilla and chimpanzee. J. Mol. Biol. 180:767-84.
 Bapteste, E., Susko, E., Leigh, J., MacLeod, D., Charlebois, R.L., and Doolittle, W.F. 2005. Do orthologous gene phylogenies really support treethinking? BMC Evol. Biol. 5:33.