The shot of the attacking green Keelerak spider is repeated a handful of times, even when another type of spider should be shown. In this shot, Toa Whenua's hand is seen holding the spider back, so when the shot is repeated, his hand is still there, even though he himself isn't.
Keetongu reaches down from atop his sitting place to cling fists with the Toa, even though we can see in other shots that he's far too high up to be able to reach them.
When the Toa are walking towards the Great Temple, Matau brushes forward between Nuju and Onewa. In the following shot, Matau is suddenly much farther ahead, already having run past Nokama and Whenua too. He's talking all the way through, so we can't assume that a few moments have been cut.
When the four Toa and the Rahaga are surrounded by the Visorak army, they are still fighting in one shot, but are standing still and closer together in the following shot.
When Sidorak says "Is that so?", the "glass cover" around his eyes seems to be missing and he has two distinct eyeballs.
The huge letter 'S' behind Sidorak's throne (in Bionicle's font) is erroneously flipped and thus doesn't match any letter in the Bionicle alphabet.
The supposed reflection of Matau in the water is not a mirrored image, so it looks just like the original Matau. This is because it's not really a reflection: we are seeing Matau through the water.
In basically all the shots with Visorak climbing on webs, their feet do not touch the webbing. In some cases, it is absolutely clear that the creatures are walking in space, as there is no webbing placed under them at all.
When Roodaka fires a blast from her clawed staff, the staff floats in the air instead of being held in her hand, with the handle visibly passing into her arm. As the staff shakes, Roodaka's hand is still motionless, and the tool passes through her arm completely.
After the Visorak lieutenant brings news of the Toa's survival to Roodaka, and the latter angrily approaches the Visorak, the shadow effect on Roodaka's body seems to be "shifted" to the side, creating the illusion of shadow hanging in thin air.
When the characters are seen from certain angles, pieces of their armor aren't attached to their bodies. When Whenua shouts "We came here to save you!", his crotch plate is clearly floating in the air. In other shots, it is obvious the characters don't have anything under their shoulder armor, even though from the outside, muscle tissue is visible underneath the armor.
Right after Roodaka notices that something is climbing up the Coliseum, the camera quickly pans over the building's side, and zooms straight to Keetongu who is indeed scaling the structure. Partway through the shot, a thick wall of some sorts obscures Keetongu, yet because of a strange error in the animation, Keetongu is visible as a small yellow dot through the wall.
Right after the shot of Vakama widening his eyes, just before Roodaka says "The Visorak horde is countless...", there is one extraneous frame in which Roodaka is standing in a different position than in the following shot.
When Matau says "Nice ship!", there's a strange dark outline around the spheres that Keetongu's carrying.
When Vakama blasts Matau off the webs, the shadow of the webs only starts moving after the blast has passed, and instead of fading out together with the light-source, the shadows seem to be "wiped away".
When Norik introduces the rest of the Rahaga, Kualus' foot appears at the top of the screen between frames and hovers there before it's time for him to make his entrance.
In the first shot of the Toa entering the ruins of the city, there's an unusual dark line on the top of the screen where the background can be seen instead of the fog.
Upon entering the ruined temple, Whenua says "Total destruction" without moving his lips.
When climbing after Vakama on the top of the Coliseum, Matau shouts after him with his mouth closed.
Nokama's mouth isn't lighting up when she begins her "Yes. The sooner we do that..." line.
Norik's lips don't move when he beckons the Toa to follow him into the temple.
When the four Toa and Norik begin their island-wide journey, they start out at a huge forest with several grassy hills in the distance. But there is no such place on the island. The map shows that they're in the Ga-Metru district, which is made up of water canals and buildings.
When Roodaka slices a splinter out of Makuta's crystal prison, she is face-to-face with him. But the crystal is on a rock wall way above any surface she could be standing on. Perhaps the original idea was that she's riding her mutated Nui-Kopen wasp during this scene, but the wasp has been deleted from the movie.
The Rahaga get hit by the Kahgarak's blast even though they could have flown upward to escape it.
If Roodaka wants to free her master Makuta from his crystal prison, why doesn't she just break it apart instead of setting up a complicated scheme? The very first scene even shows her slicing a splinter out of it with her bare fingertip. The books do explain that it is impossible to break the prison by force, and even scratching its surface required so much effort that it almost caused her to die, but this movie ignores any sort of explanation and makes it look like she scratched the crystal easily, making this a plot hole.
The five Toa stay behind to guard the temple while the Rahaga explore it, reasoning that their mutations would tarnish the temple's sanctity if they went inside. Yet the following morning, they're marching toward the temple with no qualms. The movie also doesn't explain how Vakama could break into the temple if the others were guarding it.
Norik's explanation about the Hordika mutations representing an ancient, primal state makes little sense, because the Bionicle characters didn't evolve, they were created or built and were always civilized.
Norik jokes about his oldness when he says "age makes us loud as well as wise". The problem is, Bionicle characters don't technically age. Norik and the other Rahaga are just as old as the movie's other characters, and they only appear "elderly" because they were mutated by Roodaka's powers, not because they aged.