"*** UPDATE *** After reviewing the tapes, NBC determined that an open mic picked up a whisper from the audience. It is unclear who it is that says it, but it was not said by any of the candidates"
So according to them it was an open mic in the audience. Did you hear how clear the whisper was? These mics are at least 10 feet away from any audience member and are not highly-sensitive mics. And for some reason the mic is only on just before Romney has to answer.
Well the whisperer/prompter could be in the audience, why not? And there was a local journalist in the audience who got to speak i think (i haven't seen the whole debate so i'm not sure) who had a microphone and possibly more. But obviously MSNBC contacted these people to make sure the whisper was not coming from one of them. Their conclusion is an open mic.