In a few scenes where the flying squirrels say "Swagger!" their mouths don't move.
When the squirrels sing in one scene, their mouths don't always move correctly.
In one scene, Speed says "Hey batter, batter!", but his lips don't match the line at all.
Boom mic visible
When The Forbidden Arts corners Odette and gets ready to kill her, if you watch closely at the top of the screen, you'll see what appears to be the shadow of a boom mic.
Odette's eyes change shape and color in a few scenes, when they're not supposed to.
In one scene in the movie, Roger wants to become Alise's teacher, when the other movies never mentioned him having any interest about schooling kids.
In an early scene of the movie, when Derek saves Odette from almost falling off a cliff, while they're on their way back, the scene immediately switches from day to night in a matter of 2 seconds.
Odette's necklace disappears and reappears in a lot of shots throughout the movie.
When Alise gets kidnapped by the flying squirrels, Derek and Odette chase after them on horses. In one shot, Derek's on Odette's left side, but in the next shot, he's on the right.
This movie tells the audience about a corrupted prophecy about the Swan Princess bringing darkness and despair to the world, but yet it's never mentioned in any of the other movies in the franchise.
How did the scullions ever managed to find the corrupted prophecy?
When he came from the underworld, the movie implies that The Forbidden Arts has infinite power. Then why can't he stay out of his crystal for more than 2 minutes? Why does he even have a crystal to get more power?
When Alise gets kidnapped by the flying squirrels, Derek and Odette chase after them on horses. You can clearly see that the camera and backgrounds move, but the horses are running in place.
In one scene, Derek and Odette look like they're floating on the air rather than actually walking.
A lot of background characters tend to freeze throughout the movie.