“While it is possible that the FBI discovered some vulnerability in Tor that was not disclosed in the criminal complaint, it seems much more likely that this was old-fashioned police work. Dread Pirate Roberts made a number of errors, according to the FBI, including connecting to the Silk Road server using only a Virtual Private Network and not Tor and using an email address that contained his real name in a way that could be traced back to Silk Road. The police even intercepted a Silk Road package containing nine pieces of fake identification with the photo of the man they eventually arrested.”
Source: The FBI busted Silk Road, but not the ‘dark web’ behind it | The Verge