They've bugged nearly all of the entrance and exit nodes. This allows them to do trivial traffic analysis. Parallel construction hides the method from the courts which would be reluctant to rule against anyway.
The failures of modern crypto (and historical) are almost always usage bugs, not the technology itself.
During the Government’s investigation, which was conducted jointly by the FBI and HSI, an HSI agent acting in an undercover capacity (the “HSI-UC”) successfully infiltrated the support staff involved in the administration of the Silk Road 2.0 website, and was given access to private, restricted areas of the site reserved for BENTHALL and his administrative staff. By doing so, the HSI-UC was able to interact directly with BENTHALL throughout his operation of the website.