As I said earlier, without providing evidence or explanation, the big flaw was that the server kept the messages in the clear. A recent news report has confirmed this from official sources:
The complaint says “an image of the Silk Road Web Server was made on or about July 23rd, 2013, and produced thereafter to the FBI” as a result of a request made to a foreign country under a formal MLAT.
“An image of the Silk Road Web Server was made on or about July 23rd, 2013.”
That image, or bit-for-bit copy, of the Silk Road server gave authorities access to private messages between the Silk Road’s owner and other members of the site. It was instrumental in seizing the site and arresting Ross Ulbricht, the man police allege was behind the Silk Road.