If you had bothered to read what you linked, you would have read that the system has grown so big and unwieldy that it's unlikely that the government was even aware it was being "sniffed around". The whole point of the series is that the counter terrorism arm of our government is out of control; that parts of the system aren't even aware what other parts of the system are doing. It's more or less, a bureaucratic nightmare. Considering the paper is based in the same area that most of the employees live in, it's not unlikely that after two years of investigation, they gained access to key personnel, records, etc.
Y'know, basic journalism, which is something the paper is known for on a global level, bro.
