In their court filing, the FBI says the IP address of the server was "'leaking' from the site due to an apparent misconfiguration of the user login interface by the site administrator." The agency then exploited this bug to obtain the server's location.
The FBI found a way to use that login page to produce an IP address that was not hidden by TOR standards, and then used that IP on a regular browser. That IP then produced some code from the login page, confirming that it was in fact the true location of the Silk Road.
If the court agrees with the FBI's claim, the alleged Silk Road operator may have a tougher time defending his case.
Silk Road Prosecution 4th Amendment Rebuttall by Andy Greenberg