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?
Upon having his life saved by the Scarabax beetle Click, Mata Nui states that "before this day, he has never needed help from anyone or anything". This is not entirely true, for much of the Bionicle story leading up to this point had been centered around helping him, awakening him from his coma and even resurrecting him. And it has been hinted at that Mata Nui had been semi-conscious in his comatose state, so he should by all means know that others had been trying to help him all along.
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.
When the Bone Hunters ambush Kiina and Berix, and Berix pulls out the shield Kiina told him not to steal, Kiina gets angry at him. But Berix carried the shield very visibly on his back when Kiina was following him just moments ago, so she should have noticed that he had it with him.
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, we can see that the island of Mata Nui is alive with lush vegetation, and all kinds of tropical trees and other plant-life can be seen in a handful of scenes. When we are treated to a bird's view of the island, it is clearly green with snow covering its mountains. However by this point, the mechanical 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 like in the movie.
In the opening scene, the Mask of Life flies behind entire planets, yet we can still clearly see it. It also turns around the planet of Bara Magna, and still remains visible. Compared to the planets, it should not even be seen. Thus it appears like it's about country-sized in certain shots, but after it lands, it's as big as a regular mask.
When Mata Nui asks Kiina why she is speaking against the Great Beings, there is a small dot on the back of Kiina's head which isn't supposed to be there. It's also visible in another shot seconds later.
When Mata Nui and co. leave Vulcanus, the mountains in the background look completely different from when he arrived there the night before. In particular, the giant rock arch that was at the horizon is now much closer and much smaller, and the rock outcrops that were there before are gone.
When Kiina yells to Mata Nui during the fight in the canyon, Mata Nui looks to the left side of the screen, even though the others are on the right. He's also facing the wrong way when he responds to her.
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?
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.
In the canyon scene, 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 towering Skopio beast. Even though they needed to reach the village as fast as they could and the Skopio in front of them wasn't moving forward at all, Kiina decided to drive their vehicle right into the beast, which ends with 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. Why did Kiina choose to drive to the beast instead?
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.
Due to the design of the characters, it is inevitable that sometimes they twist their limbs and other body parts in impossible ways, and so it is understandable that the viewer would find certain shots in which the character's armor bends or parts of it pass through their body. Though other instances, like Raanu's left arm sinking into the side of his torso, or Metus' arm passing into his large shoulder pad, are 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 beneath the sea in the introduction scene, the ocean around him doesn't stir up much, in fact the waters seem to be almost perfectly still. Such a gigantic robot (circa 44 million feet in height) should have caused massive tidal waves, not just a large amount of foam in the ocean. One could assume the robot was so big that waves couldn't possibly be seen when he is on camera, but that is not the case, as the animators drastically scaled him down, which caused another goof: namely, the robot could easily reach up to space (as it was shown in other media depicting the event), but in this movie, we see clear blue sky surrounding his head.
Before Kiina jumps into Ackar's house, you can see her dark silhouette standing in the doorway. As she jumps in, now perfectly visible and fully colored thanks to the lighting, she actually appears from behind the silhouette, which gradually disappears as she comes into view.
The shadow of Berix, as he runs through the hot springs, is animated in a really awkward way, and doesn't reflect how he actually runs. The legs on his shadow for instance swing forward and backward unrealistically.
You can notice a layering error in the scene of Strakk fighting Mata Nui. Strakk puts his left foot on a rock, Mata Nui waves his shield around, and at one point, you can see the shield passing between Strakk's foot and the rock. It overlaps the rock but not Strakk's foot.
The shot of Metus and Raanu speaking about Mata Nui's qualification as a potential fighter also has a layering issue. Raanu is sitting in the background, Metus is upstage of him, yet his hands pass behind Raanu.
In the wide overhead shot of Metus and Mata Nui speeding towards Vulcanus in their chariot, the vehicle is visible as a dark silhouette through the various giant LEGO pieces jutting out from the cliffs above them.
When Ackar says "Then he'll pay", the spikes on Kiina's arms are flaring outward. When the shot cuts, they're lying flush on her arms. Also in this shot, Ackar's right arm seems to be clipping through Kiina's staff.
During the argument at Tesara's arena, the animation model of Raanu's right hands get bizarrely messed up. The ball joint that his thumb attaches to is on the wrong side of his hand, so his thumb looks like it's just floating there. It stays like that for the next scene also.
A huge army made up of Glatorian, Agori and battle chariots appear to battle the Skrall and Bone Hunters. After this shot, the "army" completely disappears and only the main characters are seen fighting and defeating their enemies alone.