The U.S. Department of Defense is no longer sharing information, regarding its foreign spies, with the CIA. Years ago, because the CIA recruited the majority of foreigners as agents and sources, it established the InterSource Registry. All other branches of the U.S. government that hired foreigners for intelligence work had to register the agent with the CIA's  InterSource Registry. This was so that the CIA would not try to recruit the same source for the same work, or if the CIA did, it would be done on purpose. But the military never trusted the CIA with this information, and are now able to ignore the InterSource Registry, and instead log in the new agent with a Department of Defense database called J2X. If the CIA thinks they have a problem with a foreigner they are hiring, or have hired, they can ask the Pentagon to check their J2X list. But theres more to all this. The Department of Defense never got the kind of intelligence services they expected, or needed, from the CIA, and have been gradually increasing their own intelligence capabilities. In Afghanistan and Iraq, military intelligence operators have been hiring thousands of local agents (as informants, spies, or armed mercenaries), and have a better idea of whats going on at the ground level than the CIA does. The Pentagon does not want the CIA people to come in and screw up their agent networks. So the InterSource Registry is out, and Department of Defense control of their own foreign spies is in. 

The new DNI (Director of National Intelligence) is already being lobbied by the CIA to get the Pentagon to resume using the InterSource Registry. Thats going to be a tough sell, as the Pentagon has been able to go straight to the top to get permission for J2X. The attitude appears to be, if the CIA wont do the job for the Pentagon, then let the Pentagon do it for themselves.