When Vakama takes a last look at Metru Nui, the other Toa are missing from the background.
Vakama falls onto Lhikan's shield with his back, yet in the following shots, he is lying on it on his stomach. He had no time to roll over, as he would have fallen off that way.
There is a minor editing goof that occurs during the final confrontation between Vakama and Makuta. After Makuta pulls a chunk of rock towards himself and smashes it to pieces, the shot ends with an odd frame that doesn't correspond with the following shot. Makuta can be seen standing in a totally different position from the waist-up, whereas the next shot is a closeup of his face.
The characters react with shock when Matau's blades turn into wings and save him from a fall. However, in the comics, he has already used his blades for flight a while earlier, and the movie was meant to follow the events of the comics.
When Matau crashes the ship into the giant water-pillar, the ship is flying upwards into the air, even though in the previous shot, there was no indication that if was moving upwards. In fact, since the ship cannot fly and nothing was shown flinging it into the air, it doesn't even make sense for it to be flying in this scene.
When Nokama and the other five Matoran walk up to the Toa Suva in the Temple, she places her Toa Stone into the Ice section of the Suva. However, she is a Water Matoran, and becomes a Toa of Water afterwards (so using an Ice power to achieve this would be impossible within the laws of Bioncle). The correct Matoran to use the Ice section would be Nuju, who is an Ice Matoran.
All the metrus (regions) of the city of Metru Nui, bar Po-Metru, are written without hyphens, which is an incorrect spelling.
In one of the close-ups of the Kikanalo beast roaring at the Vahki soldiers, you can see that the red light-effect of his eye "shifted" to the side, and continues to glow next to his eye.
In the Great Temple scene, when the six chosen Matoran find each other, Nokama is walking down a staircase. The camera then lowers to focus on Onewa. The staircase remains visible, yet Nokama cannot be seen coming down on it, even though the light given off by the stone she carries is apparent. Her animation simply stopped as she got out of screen.
As Lhikan says to Nidhiki "You lost the right to call me brother long ago", two fingers on his right fist look like they're each missing a digit, or if they were "tucked back" into the armor covering his hand.
As Whenua places his palm on a capsule to free the Matoran inside, the capsule seems empty, because you can't see anything through the window on its lid. But as the lid slides away, the Matoran becomes visible.
When Toa Matau gives up his Toa power by awakening the Matoran and turns into a less powerful Turaga, the head of his Turaga form's animation model (more visible in 16:9 wide-screen) is painfully twisted to the side, rather than facing forward like it should.
When the pillar of rock crashes onto Onewa, you can see that there is a water-symbol carved into it. But the scene takes place in Po-Metru, the district of stone, not water. It should be a stone-symbol.
Nokama shouts "Hang on!" when the flow changes direction inside the chute she, Vakama and Matau are traveling in. The chute is filled with liquid, and they have to hold their breaths, so she wouldn't have been able to shout.
Nokama turns to Vakama with a very bitter and angry expression when Turaga Dume dismisses his suggestion that collecting the Great Disks would prove that they are capable heroes, even though she was the one who supported Vakama in the first place and convinced the others to go looking for the Disks.
When the three escaped Toa arrive at the platform's edge, they are shown standing in the middle of the metal frame at the platform's tip. But since there is a wide gap between the platform's base and the bar that they're standing on, technically they should be standing on the sides of the frame not the middle. They are also seen moving forward before the stop, making it look like they magically crossed that gap instead of circling around it.
When Nuju discovers his Great Disk, his hip and torso are moving wholly separately and his midsection stretches like rubber.
When Toa Lhikan arrives in the district of Ga-Metru, a male voice gasps his name, even though there are only female citizens in Ga-Metru.
When Turaga Dume says to Vakama "Matoran one day, Toa the next?", his lips are actually animated to say a longer line: "Matoran in the morning. Toa by the afternoon." This was the original line written for the scene, but it was later changed after the animation had been finished. Hence, Dume keeps moving his mouth after he's no longer speaking.
In several instances, the characters' mouths do not move when they talk.
In the Great Temple, when the Toa discuss their next move, a shot in which all of them are seen from above is shown twice. Vakama's mouth moves both times, but it is actually Nokama who's speaking when the shot is repeated.
In the tunnel scene, right before the two separate Toa teams meet up, Onewa repeats his "I'm the one suffering here!" line from an earlier scene, and Whenua also repeats "This whole thing is a load of duty if you ask me!" from another scene. These lines have no reason to be here. They were probably copied here to break the silence and were meant to sound like random murmuring. But they are still audible, and so they awkwardly stand out, since the characters aren't moving their lips and the lines make it sound like they're saying completely random things.
When Nidhiki and Krekka harass a green Matoran (Kongu, as revealed by the credits), the scene takes place in an chute-station in the ice-region of Ko-Metru. This doesn't make sense, as Kongu works in a Le-Metru (air-region) station, and he is also a Matoran of Air and not Ice. In the novelization, this scene correctly takes place in Le-Metru.
Between breaking out of the Coliseum in the middle of the city, and reaching the Great Temple in Ga-Metru on the east side of the city, the heroes can be seen driving their transport vehicle through a village in Po-Metru. However, Po-Metru is situated up north and wouldn't be en-route to Ga-Metru.
A major theme in the movie is that none of the Toa know what their mask powers are. This makes little sense, seeing as their leader Vakama worked as a mask-maker, was in fact the best mask-maker city-wide, and thus should have been more than aware of what their masks powers were.
When Turaga Dume says that finding the six Great Disks isn't enough to declare them the city's protectors, all the Toa throw their Disks to Vakama in disappointment, Whenua even declaring "What a waste!" However, the movie was meant to tie into the BIONICLE comic and novel series, in which they had used the Disks to save the city from the evil Morbuzakh plant (which has a cameo earlier in the movie), so they should know that the Disks were indeed worth the time to collect.
The Vahki fall to their doom when Nokama lures them into a trap, even though they can technically fly.
Turaga Dume commissions the Mask of Time from Vakama. Yet even after he finds out that Dume was actually the evil Makuta in disguise, for some reason he still continues crafting the mask. Why did Vakama make the mask if he knew the villain wanted it so bad? If he left it unfinished, that would have thrown a wrench into Makuta's evil plot, as far as he knew.
At first, Makuta claims that he must have the Mask of Time. In another scene, he gleefully monologues that he doesn't need the mask to win. He even attempts to sink the ship that the mask is traveling on. Then, when he steals the mask but loses it thanks to Vakama's doings, he becomes enraged about it and tries to kill him. So, does he need the mask or not? Makuta keeps contradicting himself.
Vakama reacts with amazement when the two Great Disks in his hand merge into one. He is a mask-maker, merging two or more discs to make masks out of has always been his job, so he shouldn't be so surprised in this scene.
Whenua somehow knows that Vakama was the last of them to be visited by Toa Lhikan, even though Vakama never told that to anyone.
Whenua complains "When I woke up, all I had to worry about was cataloging", apparently suggesting all his adventures as a Toa happened within the span of a single day. But according to the wider Bionicle canon, at least a month has passed since then by the time this scene happens. So unless Whenua spent that whole month awake or if he was just being ironic, his sense of time is far off.