Comment by nostrademons

Parallel construction. They use their real methods to identify the user, then once they know the user, specifically target them with simpler known methods to build evidence for the case. In the court filing, they present evidence that they've gained through known methods which don't work all that well unless you already have a suspect, but they actually caught the suspect using methods that are not public (and won't become so, unless there's an internal leak at the FBI).