Bionicle 3: Web of Shadows

A humorous scene was cut from the movie. As the Toa get ready to sleep outside the Great Temple, Matau's animal side begins to take over and he instinctively tries to build a nest, but he doesn't understand why. He also talks to Nokama (the female Toa) about their bestial "urges" and asks her if she has any urges that involve him. The scene then ends and we don't find out her answer. Since this scene was pointless and had a slight sexual undertone, it got cut, but it's included in the movie novelization. A later part of the movie also references this cut scene when the Toa discuss what they heard the night before. Nuju says he "found the sounds of the night fascinating," which shocks Matau and he quickly changes the subject. Presumably, Nuju accidentally overheard Matau behaving like an animal, much to Matau's embarrassment.

In the companion book and an early version of the script, Roodaka talks to the captured Makuta by riding a mutated Nui-Kopen (a kind of giant wasp) out to the sea to the body of Makuta. In the film however, she simply talks to a stone representing Makuta inside her chamber. Whether because of technical or financial difficulties or time restrains, the Nui-Kopen ride had to be neglected, but according to story writer Greg Farshtey, it is still considered to be canon.

According to Greg Farshtey, the appearance of the characters in this movie is not canonical. For instance, the main characters, the Toa, only have one hand in their mutated form, while their other hand is permanently turned into their weapon. In the official story, however, they had two real hands and carried a pair of weapons. Another discrepancy is the helicopter-rotors on the backs of the Rahaga characters, which allow them to fly. In the canon story, they traveled by swinging on vines and spider-webbing, or by grabbing onto the flying energy spinners they launched. In the movie, the rotor packs were only added to them to keep the pacing smoother and allow for more dramatic scenes.

Kualus' voice actor, who only says one word, is not credited. He does receive more dialogue in the mini-film BIONICLE: Shadow Play (2005), however he isn't given a credit there either.

One major difference between the movie and its novelization (which was likely written according to an earlier version of the script) is that in the novel, Vakama joins the villains to free the Matoran alone, and only turns fully evil when he touches the Makuta's throne and its dark energies corrupt him. In the movie, he instantly becomes evil upon joining the villains and never touches the throne because he gets interrupted. The throne itself isn't referred to as having belonged to Makuta either in the movie.