This sounds like incidental corroborative evidence. It hardly seems like it was what "brought down" the site, as claimed by the linked.
The site was likely brought down because the FBI or others found the server and took an image of it, and everything else seems to be backtracking corroboration from that. How did they find the server? Well therein lies the mystery, and it is likely because the FBI and other three letter agencies have a very strong interest in Tor, almost certainly having thousands of nodes that can statistically winnow down to real IPs.
The site was likely brought down because the FBI or others found the server and took an image of it, and everything else seems to be backtracking corroboration from that. How did they find the server? Well therein lies the mystery, and it is likely because the FBI and other three letter agencies have a very strong interest in Tor, almost certainly having thousands of nodes that can statistically winnow down to real IPs.