Politics
Just like Des dieux et des hommes (Of Gods and Men), I think this film has some seriously questionable politics. I know the director chooses to ignore real life and focus on the spiritual, but for me the spiritual informs the political. And you cannot have one without the other.
I was alright with it up to the moment when Julie says to Vasco 'Come live with me in France, I'll teach you French'. If she is supposed to be doing a good deed then instead of taking Vasco out of his culture and away from his family (who I'll admit are very distant from him) could she not have simply stayed in Lisbon? I mentioned Of Gods and Men, and to me The Portuguese Nun also seemed to suggest that French cultural influence is inherently good and should be spread around the world. What the Portuguese will make of a French film showing some woman take away a Portuguese orphan I'd be interested to find out. Likewise the fact the Portugal seems to be characterised as impoverished and backwards, through Vasco.
Otherwise it's a well-made film.