Spero News:

Obama, in an evident "lead-up" to the meeting, met on Thursday in Washington with several Catholic journalists, answering their questions and making clear his own positions. One revealing thing that he said at that July 2 meeting: that Obama has been profoundly influenced by the late Cardinal Joseph Bernardin of Chicago, whom he came to know when he was a community organizer in a project partially funded by the Catholic Campaign for Human Development.
(...) But despite all of the possible areas in which Obama and the Pope can agree, there is at least one area where their disagreement is profound.
Abortion. Obama believes it should be kept legal; the Pope feels it is a violation of the human right to life, and so should not be legal. Obama knows he and the Pope differ on this.
He told the eight reporters that he sees "an irreducible difference... on the abortion issue... The best we can do is suggest that people of good will can be on either side, but you can't wish those differences away."

Reuters.com has more, pointing also to another difference: stem cell research.