(at around 19 mins) When Janice is left alone in her room when the other girls play outside she is seen sitting on her bed, standing up and walking to the window. Her hair changes from in front of her right shoulder to behind her right shoulder between shots.
(at around 1h 28 mins) In the barn Carol tightens a powered on incandescent light bulb in its socket with her bare fingers without even flinching. Such a bulb, even a low power one, would have been too hot to touch after having been on for a few minutes as it was in that scene.
(at around 37 mins) Sister Charlotte is shown in Romania in a full habit with the same veil as the other nuns which would indicate that she has taken final vows, yet later she is dressed like some nuns do now in a modified habit with a short veil and no wimple. In the period when the film takes place only a postulant (someone who wants to join a religious order but has not taken vows yet) would dress like that.
(at around 32 mins) There is a scene in which Sister Charlotte appears to be administering the sacrament of confession to one of her assigned charges. Within the Catholic Church, the sacrament of confession can only be administered by a priest, so Sister Charlotte would never have had any authority to hear one's confession and administer penance.
One girl walks into the room with the other girl facing her, the latter giving confession to the nun back-to-back. The girl entering the room looks to her left and right before looking forward to see the other girl. When opening the door, she would have immediately seen the other girl without needing to look either way.
Frequently in the movie, there seems to be two dolls, but it is never acknowledged. For example, the police take away the doll, but later, the same doll, or another doll, is back in the closet surrounded by pages of the bible. It's very confusing. Is there one? Or two? This is not like Chucky where the doll can run back into place somewhere.
(at around 21 mins) After the prayer said by Mr. Mullins before the meal, Sister Charlotte does not make the sign of the cross as any good Catholic would. Neither do the girls nor Mr. Mullins, but people who say grace before a meal don't always do this.
At 1:32:43, as Linda is trying to escape in the dumbwaiter, you can clearly see someone's hand at the edge of the entry/exit area in which she's climbing towards in an attempt to get away from the demon. This is most likely someone who's supposed to be just out of scene to assist the actress if needed for safety reasons.
At one stage action is taking place in a basement the characters move past an electrical switch on a wall of modern design.. This are called 'Surface Switch' a plastic box with a dial like switch to 'ON or OFF. This design would not have been available in the time era of the movie.
(at around 1h 25 mins) When the girls try to escape in the pickup toward the end of the film, they are shown attempting to start it with a steering column-mounted ignition switch. That type of switch wasn't common until the late 1960's. The 1940's era truck in the film would have the ignition mounted on the dash.
(at around 1h 25 mins) When the girls are trying to escape in the truck, it would not have had a solenoid starter. The starter would have been a stomp starter on the floor next to the gas pedal. Chevy pickups used stomp starters until 1959.
(at around 1h 4 mins) When Janice is pushed by some sort of demon nun into the barn, she screams loudly but the other girls don't seem to hear it. However, when she screams inside the barn, they suddenly hear it.