When the Rainbooms levitate from the ground in the final battle, Twilight's extended ponytail is missing.
Many times throughout the movie, Adagio's gloves change from finger-less ones to ones that have one large hole that most of her fingers fit through.
For about a frame, while the Dazzlings sing horribly, Sonata's pendant suddenly appears around her neck intact.
Twilight's cutie mark changes sides on her skirt throughout the film.
Sunset Shimmer's cutie mark disappears from her shirt when the Rainbooms are seen walking to Principal Celestia's office.
When Adagio hears the Rainbooms in the final battle, she suddenly has her human ears as well as her pony ears.
When the Dazzlings were transforming to their half-siren state, the cracks appear out of Adagio's and Aria's necklaces, but with Sonata, the cracks spread from her shoulder instead.
In a pan-out shot of the school, a bird can be seen hovering in midair, revealing it to be a picture rather than an actual background.
After Sunset says, "The old me really was just awful, wasn't she?" Rarity can be heard saying, "Mmm...horrid," but it is Applejack who mouths that line.
During the Rainbooms first song "Better then ever" after the Mane Five Pony'd-up, Fluttershy has her pony ears as well as her human ears.