Ass Pull: The key that was considered important throughout the movie was destroyed, but one of the Care Bears was able to create a new one easily.
Hilarious in Hindsight: When you notice Nicholas zap the crowd into un-caring...you can see someone who looks suspiciously like Daria in the crowd. Gee, wonder she's such an apathetic high schooler...
In addition, this movie came out almost three decades before Magical Girl Lyrical Nanoha A's had a Book of Darkness as an antagonist (though it turned out to be much more heroic than previously thought at the end).
Jerkass Woobie: Nicholas may be the antagonist for most of the film, but come on, can we be too hard on him? He never had a friend in his life!
Society Marches On: The orphans reciting their evening prayers in the opening scene comes across as decidedly quaint today. Sure, this might still happen in some families, but with society becoming increasingly diverse and secular, including such a scene in a children's cartoon can seem dated and - by modern standards - inappropriate in the 21st century.