Kopaka's shield is normal-sized in the cutscenes, but when he has to use it as a snowboard, it suddenly becomes gigantic.
In some shots of the opening cinematic, Gali can be seen in her Nuva form. This isn't right, since she only transforms into a Nuva much later on. The rest of the animation correctly shows her in her original pre-Nuva body.
Takanuva is mistakenly called "Takua Nuva".
After defeating the brown Rahkshi, it loses its Kraata slug, the thing that kept it alive. However, instead of a Kraata, they animated a Krana into the game, a totally different type of creature that resembles a mask instead of a slug.
All the villagers of Ta-Koro, the village of fire, are colored green instead of red. In reality, only the denizens of Le-Koro, the jungle village of air should be green. In the game's beta version, the Ta-Koro residents are correctly colored red, however the colors were swapped in the finished release.
The plural of Matoran is constantly spelled as "Matorans", even though technically, the name is not supposed to have a pluralized form in English, so it should simply be "Matoran".
On the PC version, Turaga Nokama's face textures in Gali's level are messed up: she appears with a disturbing red smudge instead of her face. As well, her animation bones are also visibly clipping through her character model.
In the character descriptions as well as promotional images, the Turaga elders have their animation bones visibly poking through their CGI models.
The Bohrok-Kal can tunnel underground, even though the ground they're on is clearly shown to be solid rock. They sometimes even "tunnel into" the large drain-cover, which would be impossible, since it's not even a solid structure and there's only water underneath it.
Similar to how the red Fire Matoran have been replaced with green Air Matoran in Tahu's level yet the icon on the lower right still shows red Matoran, the same icon appears in Lewa's level even though the Matoran there are green.
In Tahu's level, when the villagers begin constructing the wolf-like animal, Tahu walks out of the sanctuary over to Vakama while moving his mouth, but he doesn't say anything.
When you lose on Kopaka's first level, the cutscene shows the Gahlok burning your village. However, the Gahlok controls water, not fire, so this scene makes no sense.
Tahu tells Kopaka to target the Krana within the bodies of the Bohrok, since those are their weakness. This has no follow-up, and the game requires the player to simply blast the Bohrok wherever they can hit them.
It is not explained how or why the Toa turn into Toa Nuva. After Kopaka defeats a couple of Bohrok, all of the Toa suddenly appear in a white area and somehow the power of the Krana transforms them into powerful Nuva forms. It is also not shown how the Bohrok swarm is defeated. They disappear between levels after you only beat a few Bohrok.
In the story, the Bohrok-Kal's mission is to free the Bohrok queens. However since the queens never appear in the game, it's not explained why the Bohrok-Kal show up, nor just what they even are.
The purpose of the Rahkshi is to go after Takua the Chronicler and keep him from finding the Seventh Toa. But in the game, the Rahkshi first appear in Onu-Wahi and Le-Wahi, two places that Takua doesn't even visit.
German language version: Pohatu mispronounces Turaga as "Taruga".
In the first fire level, Tahu rescues green Matorans. The green Matorans are from the jungle zone as later seen even. He should be rescuing red Matorans (as seen at the corner of the screen every time he rescues one).
When the Chronicler is telling Tahu about the Seventh Toa, the text box begins with "A Toa of Light", but the Chronicler never says this sentence.