The "hacking" was speculation on the defense's part when they filed their motion in August. If you read the motion[1], because the defense didn't yet know how the FBI located the server, Ulbricht's lawyer wrote a long statement speculating that the NSA/DEA was providing the information to the FBI through parallel construction. The defense did not show any proof of their accusation.
A month later, the FBI gave sworn testimony[2] indicating that they found the server because Ulbricht had failed to configure it properly and it was leaking out its actual IP outside of Tor channels. There hasn't been any proof shown that the FBI hacked his server. A number of people have claimed in the past that they came across the actual IP for Silk Road's server as a result of misconfiguration[3][4], so frankly it doesn't surprise me at all that the FBI also found a leak.
Have you actually read [3] and [4]? Based on the comments, the two posts (Made by the same person) were from a notoriously anti-Bitcoin troll on the day that market prices were at an all time high.
I was with you up until I actually read the posts, which I suspect you did not.
I agree [3] looks that way, but [4] certainly doesn't. The thread is filled with people who saw the debugging screens. I think this user's post history is the most informative:
