I don't see how the Vatican doesn't deny it. They can't be seen butting into the middle of a nation's election, it sets all kinds of horrible precedents. Bernie should know this isn't a good thing to be doing, it's foreign policy 101.
They won't deny it if they actually met. They may comment on the circumstances but won't do any big bold statement.
It's not the first time a pope is been tricked into a kind of endorsement but not really. It's been done way way WAY worst. When pope John Paul II went to Chile and met in private with Pinochet to petition for the safety of all political prisoners. He was tricked into thinking that behind a door was the meeting room when it was in fact the main balcony to the street.
The picture of the pope in the balcony with Pinochet at his side waving to the thousands gathering outside was used as regime propaganda. He didn't left the balcony, he smiled an waived.
It's not on the same league, and it's not the same pope. But the Vatican has his own special ways and I don't think they will make any bold statement either way. Just confirm what occurred: They met while the pope was leaving.