These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Ass Pull: The Finale of the sequel. Specifically, the reactions of the Archdiocese at the end of the film don't match their reactions during the musical number by a long shot.
Cliché Storm: Sister Act 2's plot is basically the quirky teacher that the strict authority figures don't get her style of teaching, but she helps the troubled inner city students believe in themselves, then proves all the stuck up authority figures wrong, and saves the school from the corrupt corporate executive, by winning a choir contest.
Genius Bonus: There are a lot of Catholic in-jokes. For starters, all the songs the sisters jazz up are actual Catholic hymns. Play these films to a bunch of Catholic high school students, and prepare to be unable to hear the actual film over the sound of gut-busting laughter.
Some Anvils Need to Be Dropped: Religion is capable of great things, helping and guiding people who need it the most... but it doesn't have to be strict and traditional to do it. Basically, the old ways aren't always the best, but that doesn't mean there isn't anything of value in them.
Spiritual Licensee: Of Howard Hawks' A Song is Born, which was itself a musical remake of his own Ball of Fire.