The NSA is excellent at tracking communication contacts that establish the existence of relationships (notwithstanding the potential of false positives). And this would also work for tracking someone driving around in a car running errands in specific places.

But if someone arrives in a US city unwittingly carrying Ebola and gets on a crowded bus or subway car, that's not so easy to track. Likewise if the person goes to a nightclub or other crowded place. Suppose it's a returning American who attends a baseball or football game - the NSA may well be able to ID almost everyone who attended the event, but trying to screen/isolate tens of thousands of people who might have come in contact with an infected individual wandering around a stadium is easier said than done.