The scene in question is when Simonetta Stefanelli, the actress who played Apollonia, Michael Corleone's new wife, is shown topless on the night of their wedding.
Obviously, the implication is still enough to make viewers uncomfortable, but it's nothing compared to her role in Pretty Baby.
Kubrick said afterward that, if he knew how badly he would be handcuffed by the Hays Code, he would have never made the film.