The extra footage included some additional scenes of violence, and gore, and some extremely mild nudity. Specifically:
- The aftermath of the African "attack" shows more graphically burned or mutilated bodies, making it more clear why people think Superman did it.
- At one point Bruce Wayne is shown naked from behind.
With MPAA ratings, seconds and minutes can count. A few seconds of violence might only mandate a PG-13 rating but if you add another minute of it, that might push it over into the R. They also take the totality of the movie, and if the new footage makes the tone "more violent" or "darker", then things that they let slide previously might taken on new meaning in context and the whole product becomes R.
As far as I know, the MPAA only ever shares their ratings notes with the studios, so unless WB decides to release those, we'll never more any more details.