Of note is that the software at issue, the DCS-5000 gets information from carriers after they turn on surveillance on their switches once they get a court order (CALEA mandates the switches be wiretap-compliant). That means this number ostensibly has nothing to do with the government's secret warrantless wiretapping program, or the government's data-mining of billions of call records.
Your other link was about mistakes made in 2000, before current practices, before 911, and before the current Administration was even in power.
I do understand the S/W issues but when pressed the FBI will not say what the do with the "data of no interest". In wiretapping the FBI is out of control. Virtually every bit on electronic stuff that gets into the airwaves is now recorded. Good news bad news - they have about a 5 year backlog of stuff to listen too. Computer filtering it doing most of the work but there are still years of stuff a human needs to listen too.
BTW I do think there are 4th Amendment issues here but RP just goes over top in presentation. No this isn't just a W issue; JEH tapped the hell out of this country.