According to director Jon Burton, Bionicle Heroes was originally designed to be a first-person shooter for kids. However, when the game was submitted earlier than usual to the Entertainment Software Ratings Board for review, they gave the game a Mature rating. Burton speculated that the reason why it got such a high preliminary rating was because many first-person shooters at the time were being rated Mature regardless of if there were violent elements or not like the Halo series. Burton claimed that Lego required the game to be rated either Everyone or Everyone 10+, so even bumping the game down to a Teen rating would have been considered unacceptable. They briefly considered making the game a platformer or like more traditional Lego games, but this would have required a complete overhaul in game design. Instead, Traveller's Tales shifted the game from a first to a third-person shooter. Interestingly, the Nintendo DS version of the game developed by Amaze Entertainment did end up releasing as a first-person shooter and carried a Teen rating despite Lego's requirements.

During the final boss with Vezon, after performing one final hit on him, he sinks into the lava, and as it consumes his body, he reaches his arm out to wave and deliver a thumbs up. This is a reference to the ending of the 1991 film "Terminator 2: Judgment Day".

If the player beats the final boss, Vezon, and gets 100% completion, a bonus cutscene will play. At the end of the cutscene, a whirlpool can be seen forming off the shore of Voya Nui. This acted as a hint towards the next wave of Bionicle toy sets in 2007, which featured a prominent underwater theme with new characters like the Barraki and the Toa Mahri.

The game has several .txt files within it containing long messages from the developers. One file called Wacky.txt lists a set of facts about the game.