At 56:23, Sister Cecilia is seen facing the left while she is in a wheelchair chained up, while Father Sal Tedeschi is seen walking up behind her before passing her to go to the front of the room. In the next scene, Cecilia is now seemingly facing the front of the room without having been moved.
It is not possible for human DNA in an ancient artifact to survive for 2000 years. Therefore, a geneticist can't extract DNA samples from a 2000-year-old relic to impregnate nuns.
The term "Immaculate" has nothing to do a virginal pregnancy, often considered in eg the birth of Jesus to the virgin, Mary. Immaculate has to do with "being born without sin" as in the reference to the Immaculate Mary, the Mother of Jesus, being herself born without sin.
The title and screenplay are guilty of the common misconception that the Immaculate Conception and the Virgin Birth are the same thing. The Immaculate Conception refers to Mary's own conception free of original sin.
When Sister Cecilia nearly drowned in a frozen lake and was declared dead for seven minutes, she was supposed to suffer serious brain damage because of a lack of oxygen, but there is no indication she is suffering repercussions from her near-death experience.