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)
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.
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: 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)