Character mistake: When the father gets buried alive, he rings the bell. Then, when the (almost) nun hears the bell and comes running, you'll notice she calls out for the father when there's no way she can know it is him by just the sound of that bell. (00:40:24)
Character mistake: If the nuns in the Abbey weren't real and were created by Valek, why did Valek get one of the nuns to explain to Sister Irene the exact way to defeat her?
Answer: The nun was trying to find the relic. The deceased nuns had no actual idea where it was. That's the whole reason Irene was summoned by the Vatican because she had visions about "Mary pointing the way" also the "ghost nuns" more than likely have something to do with her clairvoyance as well.