One, the pope said it, meant it about the film as conveying an authentic sense of the events as he, the pope, had always imagined them. The original impression conveyed by the journalist reports was entirely accurate. However, controversy ensued, and the handlers at the Vatican now think they were rash in going so far out on a limb (honestly). They are trying to half retract the statement, and to take the blame for that half-retraction themselves - or even (dishonestly) to put it on the journalists. Anywhere but on the pope.
Two, the pope said the words, but they had a different meaning. They were a commentary on present times, that the world has not changed. The leading "it" means the world, now. The PR types as the Vatican misunderstood the comment, took it in the previous sense (see one above), and led the reporters to believe that one (above) was true. Having made this mistake, and having been corrected internally over it, they are now attempting to retract the implication, but not the quote. Thus the weaseling you noticed, that they deny a judgment of the film, but not the statement itself.
Three, the pope did not say the words. The PR types made them up as something the pope might say, that they thought sounded right or non-commital or deep or whatever. They meant to endorse the film, knowing that was a kind of political action. They thought it would be a sort of fait accompli, they say the pope said it, nobody denies that, it passes for fact. The pope or others with his ear get wind of this, and he denies the statement. The PR types are then left scrambling to get the statement retracted, without admitting they flat made it up.
I personally think that "one" is the most likely explanation. But I can't rule out "two". I consider "three" unlikely, but the PR types are not looking very good here so it might be naive of me to think they wouldn't try such a thing in the first place (my main reason for doubting "three"). I think the PR types want us to think "two" is right, at the moment. But that may be because "one" is right, and they are trying to avoid the controversy of an endorsement, and "two" is just a cover story.
That is my analysis of it. Incidentally, another reason I think it is one or two is that the comment sounds like the pope. It is the sort of thing he'd say. Of course, his handlers presumably know that, know what he sounds like, so this doesn't really rule out "three" completely. But I think it highly likely he did say the words, and that is why the PR types initially encouraged the reporters to report them.