When the Mother Superior seduces the deaf-mute boy, he's sleeping in a tomato garden. Tomatoes are a New World crop that wouldn't be brought to Italy for another two centuries.
When Caterina sleeps with Riccardo, a tan line left by a bikini top can be seen on her back, but the bikini wasn't in use in 14th-century Italy. Riccardo's body also shows tan lines left by wearing bathing trunks. Tan lines are also visible on the sinners cast into Hell in the dream sequence.
When the cherubim are singing Veni Sancte Spiritus in Tingoccio's vision of Heaven, their lip movements clearly do not match the singing.