The shot of Makuta walking toward Takanuva is shown twice: once before their Kolhii-match and then again after it. In this shot, Takanuva already has his staff at ready, and behind Makuta, the gate of his lair is buried under rubble. These create continuity errors, since Takanuva only gets his staff out after the first time this shot is shown, and Makuta blocks the gate to his lair much later.
When the characters are waiting for the Rahkshi to emerge out of the smoke at Ta-Koro, Vakama is missing his robe in two shots: first when he, Nokama and Gali are looking at the distance, and right after Nokama says "Rahkshi".
When the Toa ready their tools for the final battle against the Rahkshi, Pohatu is holding his two-pronged claw tools. Moments later when Tahu projects a force field around the Toa, Pohatu's claws suddenly and inexplicably have four prongs.
After Takua hops onto Pewku, he pats her on the back. The next shot is a close-up of Pewku cooing, in which Takua is nowhere to be seen.
After Takanuva, while hanging off the side of a pillar hears the noise of the approaching Matoran, Turaga, and Toa, there is a close-up of him showing a desperate expression. However in this shot, he doesn't seem to be clinging on to anything, he appears to be standing on the floor. In the following shot, he is back on the pillar again.
A 'miniature' Turaga Nuju appears in front of Turaga Vakama near the end, at the Kini-Nui temple when Hahli is holding her speech. His size suggests that he should have been animated behind the crowd. When this shot is repeated again, the goof still shows.
As Jaller says "Yes, Toa Tahu." near the beginning, his arm passes through Tahu Nuva's magma sword.
The Kraata slug slips between the legs and chest of the empty Rahkshi armor suit. The entrance to the suit is on its back, so it shouldn't have been able to get into it in such a way.
As Hahli says "I'll keep that in mind", watch the crowd behind her. They are constantly repeating the same few frames of animation, and two members of the crowd near the top of the screen miraculously pop into existence between frames.
During the match, when Hewkii takes the ball away from Takua, take a look at Hahli in the background: instead of moving forward, she slides sideways and then starts running in place.
There is an editing error when the green Rahkshi attacks Tahu who's lying on the ground: it is standing in a completely different pose and farther away from view in the first frame of the shot. This jarring shift is visible when viewed in motion.
When Tahu gets up after having been blasted with water, the puddle around him doesn't seem to be resting on the ground, because when the camera moves upward, it shifts position.
The Kolhii players make many unfeasible moves. Hahli manages to jump up, start falling, and then somehow go higher again as she hits the ball. Hewkii also propels himself forward during one vertical jump without touching anything.
In several instances, just before the shot cuts, a thin line flashes up on the bottom of the screen for a frame, that actually belongs to the following shot. This happens for example when Jaller, Takua and Pewku hurry out of Ta-Koro to the kolhii match, when Gali blasts water at Tahu and the green Rahkshi, just after Gali asks "But what were they after?" or when Hahli comes out of the tunnel. In each case, you can see lines on the bottom of the screen that correspond to the colors of the next shot.
When Lewa informs Jaller and Takua of their village's destruction, the dark section of Jaller's right shoulder is halfway sunken into the shoulder joint. It "fixes itself" in the following shots.
The Rahkshi react to Kopaka before he says "Surprise!" and when he says it, his mouth doesn't move.
In several shots, the characters' mouth doesn't move when they speak, mostly when they're farther away from the "camera". Many of Makuta's shots are also reused, so often the lip movements don't match up to the dialogue.
In the beginning scene, when Jaller is first shown calling after Takua, at one point he lifts up his hand to his mouth without shouting.
After Tahu's healing, when Gali gestures for the others to stop, her mouth is lighting up when she's silent and the light fades when she says "That's enough." It should light up when she speaks.
In the caves, after Makuta leaves Takua and Jaller finds him, Jaller is moving his jaw but doesn't say anything.
Lewa leads Jaller and Takua from the jungle of Le-Wahi straight to the snowy mountains of Ko-Wahi. However, on the map of the island, these two areas don't border each other: there is a rocky, mountainous area between Le-Wahi and Ko-Wahi, which they do visit at the end of the movie.
During the Onu-Koro siege scene, Toa Puhatu gets struck by Turahk's fear power and Toa Onua gets his strength drained by Vorahk's hunger power. Onua collapses to the ground, and Pohatu also stops moving. A couple of minutes later, they are up on their feet, and join the fight fully powered. It is never explained how they recovered so fast. Toa Tahu gets hit by Kurahk's anger power, and that doesn't wear off. In Onua's case, one could assume that his strength returned by itself. Pohatu might have also recovered from the fear Turahk's power subjected him to, but it is never shown.
When the other Toa argue that they should face Makuta as a team, Takanuva dismisses them and goes to fight him alone. But once he meets Makuta, he immediately calls for the others to follow him anyway. Yet when they are down there, the Toa just stand around and gaze instead of help Takanuva defeat Makuta. None of this makes sense.
Takua fools the other people into believing that Jaller is the chosen herald. Why doesn't Jaller tell the truth? He's a respected Captain of the Guard, whereas Takua's presented as a notoriously irresponsible adventurer, so the people would obviously believe him over Takua.
In order to descend into the Makuta's lair, Hahli needed to hitch a ride in a compartment of Takanuva's flying vehicle because no one knew how to reach it. Yet later on her way out, Hahli makes her way through an enormous cave and scales an immense vertical tunnel that opens on the cave's ceiling (and is thus unreachable to anyone who can't fly) under a few moments, while also carrying a mask in one hand.
Takanuva orders Hahli to "summon the Matoran", but when she returns, she is only bringing with her the Toa and the Turaga, but no Matoran. The reason for this is that originally, all of the island's citizens (the Matoran) would have followed her underground, but the ending of the movie was changed during production. For some reason, Takanuva's line wasn't corrected.
In the Kolhii stadium, Onewa and Nokama are standing behind the banners of each other's village instead of their own.
When the Rahkshi attack Ta-Koro, Tahu boldly taunts "None have breached Ta-Koro's gates before!" However in the comics, books and online animations leading up to the movie's events, the villainous Bohrok-Kal have breached the village's defenses and even defeated Tahu.