Continuity mistake: When Father Flynn and Sister James are sitting outside on the bench, Flynn shows a book (possibly the bible) with dried flowers in it. He places the bookmark ribbon to the center of two pages. In the next shot, the ribbon moves to the middle of the left page. (01:02:05)
Factual error: When Meryl Streep is walking outside and talking to Mrs. Miller about the potential abuses of her son, you can see a basketball court in the background and on the court is a 3-point line. The movie is supposed to take place in 1964 and the 3 point line wasn't introduced until 1979/1980. (01:10:20)
Continuity mistake: When Sister Aloysius is walking Mrs. Miller to work, the Sister's umbrella handle is hooked to the left, then hooked to the right in the next shot. (01:12:10)
Continuity mistake: After speaking to Donald's mom, Sister Aloysius is standing in the wind with leaves floating in the air. The quantity of leaves situated on the ground changes between shots. (01:17:55)
Factual error: At the beginning of the movie, there is a scene showing a car driving through an intersection containing curb cuts (street-level curb corners) and painted crosswalks. The movie is supposed to be set in 1964. Curb cuts were first introduced in 1970 and not widely used until after the Americans with Disabilities Act of 1990. Painted crosswalks were not used much until the late 1990s.
Character mistake: After Father Flynn has completed his first sermon, Donald Miller comes into the dressing room and says "That was some sermon, Father." Flynn then says "Hi Jim". Jim is the name of the other altar boy. He should have said Donald.
Suggested correction: Flynn says "hey, Champ", not Jim.
Continuity mistake: During the meeting among Sisters Aloysious and James and Father Flynn in the principal's office, Sister James has turned in her chair to face the other two standing at the door and says she smelled alcohol on Donald Miller's breath. Her hands at this point are gripping the back of the chair. The camera angle changes to behind the desk, showing Sister James still turned toward the door in her chair after speaking this line, but her hands are resting on her leg.