Continuity mistake: Just before seeing Principle Celestia, and they are walking down the hallway, the cutie mark on Sunset's shirt disappears.
Continuity mistake: When Sonata's siren form is stunned by Fluttershy's butterflies, her teeth are blue when they should be white.
Continuity mistake: Shortly after the Sirens' pendants shatter, Sonata's reappears for a second.
Continuity mistake: At the start the Dazzlings see the transformation of Sunset Shimmer that was in the last movie. A couple of seconds pass and they run outside to see better and she is being defeated. In the last movie it took a couple minutes.
