How is water getting inside this waterproof roofing?

I’m managing a social business construction group that is trying to provide low cost home improvements to disadvantaged families in Peru. We recently put up a plexiforte (plastic) roof and found out later that water is getting in the house somehow. It really doesn’t rain and the roofing material is waterproof as well as properly installed. The family did seal up the windows and any open space underneath the roof. Is it possible that this lack of airflow has been causing condensation? What else could the problem be?