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.
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.
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.
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.
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.
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 has the same 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.