Thanks. But that's not completely accurate. A tracking device is soley for location - and will work inside a building; a hidden mic is just for relaying their talking.
CIA could afford to do both.
I hope this didn't ruin the movie for the OP. I still enjoyed the series - except for the stupid 'shaky cam' fight scenes. Ridiculous.
If I remember right, the CIA guys describe the basement they found Nicky in as a former bomb shelter or something like that, which was their explanation as to why they couldn't find her sooner. Basically, something far enough underground and with thick enough walls/ceiling would block transmissions.
Anyways, the point was they new exactly where the two were up until that point anyways. But, it didn't really matter. Bourne wasn't trying to escape with her; he just needed a minute to get information. So, he took Nicky underground so he could interrogate her without being heard by the others.
Then, he fled again and left her behind.