A lot of these quickly got corrected thanks to me watching and rewatching the MNOG and Bohrok animations over and over, and discovering BZPower as a literal child. 1-9 on this list were all corrected for me by a single trip to Bionicle.com in mid-2002.
Obligatory "I thought they were robots".
I assumed that all Lego sets and stories coexisted in a fantastical world called Legoland. This included Bionicle. So my earliest memories of playing with Tahu and Kopaka (before I got all the others) in 2001-2002 were about them being giant robot warriors sent from the cosmos protecting "Legoland" from evil.
I thought the Bionicle sets were in scale with regular Lego, so they were giants in a world of minifigs.
I never owned any Roboriders, but when I saw them in stores I thought they were motorbikes for the Toa to ride on.
When the commercials for the 2001 Matoran Happy Meals were out, I thought the McToran were just mini half-effort cheapo versions of the Toa. Like, Jaller was just literally a smaller, cheaper Tahu toy with a yellow mask for some reason. I guess to look more kid-friendly?
I thought Lewa was the Toa of Jungle. (I think at one point I even called him "Toa of Swamp") This was corrected by a trip to Bionicle.com.
I thought Lewa had machine gun fingers.
I thought Lewa could fly, rather than glide or channel air while using his mask.
My friend's brother, who had all six Toa Mata before any of my other friends or I did, convinced me that this mysterious white and light blue Technic set he had but didn't give me the name of was the secret 7th Toa. Looking back, I'm like 90% sure this was Ski from Throwbots (possibly modded), though said friend's brother kept him in a Bionicle-like canister assembled. (Look, I wasn't familiar with Throwbots at all back then)
I thought "Rahi" only referred to animals under Makuta's control.
When I first played MNOG, I assumed you played as a human who traveled to Mata Nui. Didn't help that you don't learn what the protagonist looks like or what his name is until literally the last couple cutscenes.
I thought flight was one of Takanuva's powers because of the 2003 console/PC game.
I thought the Rahkshi could talk.
When the Bohrok Kal first came out, I thought they were basically Super Saiyan Bohrok.
Before the 2nd movie came out, I thought Lhikan would fight alongside the Toa Metru, not be the Turaga who guides them.
For a while, I referred to Mata Nui as a Great Being, rather than as the Great Spirit. This is because I thought the "Great Beings" were just godlike beings and Mata Nui was one of a pantheon. I was corrected here on BZP in 2008 or so.
When the Glatorian were first revealed, I was expecting them to have Elemental Toa powers.
And some misconceptions from my friends and/or family:
My friend thought Lewa could shoot vines from his hand. He convinced me of this for a while.
My other friend thought that the Toa Nuva would transform back into their old Mata forms if their masks were knocked off, and could transform back by recovering their masks. We'd make believe that we were the Toa at recess, and that was always how he'd portray getting his mask knocked off.
The friend mentioned directly above somehow had this idea that the Great Spirit Mata Nui looked like a red, gold, and silver Tahu Nuva, and had some special connection with Tahu specifically.
My dad thought Onua was a villain because he was a scary dude with claws.
Man, I had a lot of misconceptions about Lewa alone. Maybe I should make a Lewa revamp with wings and an actual gun arm, Barret style.