The large shoulder armor of Strakk changes its connection to his arms between shots. In some shots, they attach to the front of his upper arms, while in others, they are on the sides.
Even though the planet that the opening scene takes place on is Aqua Magna, the Planet of the Endless Ocean, we can clearly see several large green continents on its surface. The whole planet is supposed to be covered exclusively by water, according to the Bionicle canon. The way it is portrayed in this movie contradicts everything that has been stated before.
In some shots, the animation of the tiny spinning gears, propellers, and bolts that can be found on various body parts of the characters is absent. They seem to be spinning in one shot, then suddenly stop in the next, and so on.
In the opening scene, the island of Mata Nui is depicted with lush vegetation. But according to the backstory, by this point the Bohrok swarms have already wiped or chased every living thing off the island, and demolished its surface. The island should look completely barren and lifeless, not lush.
When the door leading to the Great Beings' lab opens, there is a large cloud of dust rising with it. In the next shot, the dust is completely gone.
The Mask of Life, as it hurtles through space, is seen pulling a trail behind, like a meteor in Earth's orbit. But this is erroneous, since there is no atmosphere in space, and the mask remains perfectly intact upon crashing into a planet's surface. Then what was that trail made up of?
As the rock steed looks back at Berix who has unwittingly fallen onto its back, the wide armor plating of its face sinks into its neck slightly.
Due to the design of the characters, it is inevitable that sometimes parts of them would clip through each other. Though other instances, like Raanu's left arm clipping into the side of his torso, or Metus' arm passing into his large shoulder pad, count as animation errors that could have been avoided.
After Kiina leaps into the air and sends a burst of water from her trident at a nearby rock, she takes an exceedingly long time to reach the ground. Considering she cannot fly, nor can we notice any signs that would show she stayed aloft by bursting water underneath her, it is impossible for her to stay that long in the air.
As the camera pans through the village of Roxtus to focus on Mata Nui, Kiina, and Berix, and as a Skrall unit runs past on the left of the screen, you can notice how several Skrall are actually running in place, without making any progress forward.
As the Mata Nui robot rises up from the sea in the opening scene, the waters around him seem almost perfectly still. Such a gigantic robot should have caused massive tidal waves. Instead, it only creates quick splashes and stirs up foam.
If you watch the spinning nuts and bolts on the characters closely, you can notice that at times, they suddenly start to move choppy. Instead of making full turns, they appear from one position into the next between two frames.
As Metus says "So, we came up with a solution", the highlight suddenly vanishes between frames from the top corner of the giant BIONICLE piece in the background.
During the final fight, when Mata Nui says his "We fight with purpose" line, his right shoulder armor is detached from his arm and just floats in the air beside him.
When Strakk walks away from the arena, his right foot is inexplicably on backwards.
There is an odd flickering color on the inside of Mata Nui's thigh when Kiina says "I want out of this dump." It looks like two overlapping surfaces in his animation model causing rendering errors.
When Ackar points out how crazy it was to jump into an arena match and Mata Nui replies by saying "True", Ackar is for some reason mouthing Mata Nui's response.
When a screw falls out of Berix's arm, after having proclaimed his masterful repairing skills, you can hear it make a clinging sound before it reaches the ground.
During the rockfall in the canyon, Ackar doesn't open his mouth when he gasps.
When the audience members are yelling at Ackar to stop interrupting the fight between Vastus and Tarix, the two ice Agori are doing the exact same motions. When one shouts "Yeah, sit down!", the other one is mouthing the words, even though only one voice is heard.
In many shots when crowd members are shouting, only a handful voices can be heard even when many of them are moving their lips.
In the canyon, Kiina, Ackar, and Mata Nui are on their way to the village of Tesara, being chased by a horde of Bone Hunters and confronted by a Skopio beast. Though they need to reach the village fast and the Skopio ahead of them wasn't moving forward, Kiina drives their vehicle right into the beast, resulting in a crash. The logical choice would have been to drive past it, as there was a large opening next to the Skopio, leading straight to the village.
During the Glatorian's fight with the Bone Hunters, there is a shot in which a Bone Hunter, on top of his rock steed, is chasing Kiina. The camera pans and thus the Bone Hunter gets out of view. But Kiina stops, and for some reason the Bone Hunter never reaches her, even though he has been chasing her just a few seconds earlier. He wanted to kill her, so why would he suddenly vanish?
Mata Nui takes Tuma's green shield as a trophy for victory. Later, after he throws the shield away, he is seen carrying a red shield. Where did it come from, since it appeared before any Skrall warriors wielding red shields have been defeated? The shield stays red for the rest of the movie.
Older Glatorian are said to get banished when they don't fight well anymore. Why don't they keep them around to train newer ones? Ackar, a Glatorian beyond his prime, teaches Mata Nui how to be a good fighter within mere days.
Mata Nui claims that the Mask of Life's powers only work on things that are or were at one point alive. But his own body was created by the masks' powers from mere sand, so it obviously works on inorganic materials too.
After Click helps save him, Mata Nui states that "before this day, he has never needed help from anyone or anything". This is not true, since much of the Bionicle story leading up to this point has been centered around helping Mata Nui, awakening him from his coma and even resurrecting him. And it's been hinted at that Mata Nui was semi-conscious in his comatose state, so he should know that others have helped him too.
As Metus first meets Mata Nui, whom he initially assumes is a local, he tells him a joke about how there are lots of ruins on the planet, even mentioning the name of the planet: Bara Magna. He only learns later that Mata Nui is in fact not from that planet. So if he thought he was from around there, why did he make a point of telling him the planet's name?
Berix pushes Kiina aside to get a view at the fight scene and yell at Tuma. However since they are in a cage at this point, he was perfectly able to see what was going on form where he was standing. He didn't need to shove his companion to the side.
Not necessarily a goof but an inconsistency nonetheless: Akcar's impressive demonstration of fighting moves throughout the movie clearly contradicts Raanu's statement that he's way beyond his prime. None of the events seems to confirm the negative things the characters say about him.
Ackar claims that it's impossible for the Skrall and the Bone Hunters to work together, since they are rival tribes, even though all of the other tribes on the planet are rivals as well, yet they do work together perfectly thanks to the arena system. In fact, according to the backstory, he was one of the founders of that system, so it doesn't make sense for him to scoff at the idea of rivals uniting.