Real IP of the server was leaked/transmitted in the http headers returned to a user when an incorrect captcha was entered on the login page.
Quote:
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Ever since October 2013, when the FBI took down the online black market and drug bazaar known as the Silk Road, privacy activists and security experts have traded conspiracy theories about how the U.S. government managed to discover the geographic location of the Silk Road Web servers. Those systems were supposed to be obscured behind the anonymity service Tor, but as court documents released Friday explain, that wasn’t entirely true: Turns out, the login page for the Silk Road employed an anti-abuse CAPTCHA service that pulled content from the open Internet, thus leaking the site’s true location.
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Krebs
US declaration of how they found it (PDF)
http://ia700603.us.archive.org/21/it...22824.57.0.pdf