Reading the document, all the five presented cases are the FBI cases, not NSA. They are also listed as the FISA cases. The title is intentionally misleading.
(Hint: It's the other federal agency mentioned in the Intercept's headline. Second hint: This agency is home to the National Security Branch, created in 2005. Third hint: it's listed as one of the 17 "member agencies" of the intelligence community here: http://www.intelligence.gov/mission/member-agencies.html)
"only the Justice Department and the FBI are permitted to attend its proceedings on domestic surveillance"
That is, it looks like the NSA is the 'responsible agency' only on foreign communications, and the domestic cases are the responsibility of the FBI, even if the surveillance is carried out by the NSA.