Either one of two things happened: Bloomberg got screwed over by its sources, or the U.S. government is outright lying and clambering to save face with the already disgruntled public.
If Clapper is not lying, he his denial admits incompetence. A likely explanation? The NSA dedicates so much of its time and zillion dollar budget spying on everyone and hoarding the information that it can't find a security hole that was staring it in the face. Clapper's response instead disclosed a seismic vulnerability in the intelligence agency's own mission, to "protect U.S. national security systems and to produce foreign signals intelligence information."