After you unlock the six Bohrok in their enclosure, the game starts referring to them with names ending in "-Kal" and their descriptions in the trophy room are also those of the Bohrok-Kal. However, the Bohrok-Kal are actually separate characters from the regular Bohrok.
Some of the story facts detailed in the Trophy Cave are incorrect. They state that the Toa received their Golden Masks after defeating the Bohrok hordes, but in the story, they received them before the Bohrok even showed up.
In the trophy room, the Ta-Metru, Ga-Metru, and Le-Metru Great Disks have their names and descriptions swapped.
The trophy room incorrectly lists the Rua mask as the Mask of Valor, but in reality, it is the Mask of Wisdom. It is also shown with an incorrect design, looking like a Hau mask, however this isn't necessarily an error, since the official mask piece sold by LEGO was likewise incorrectly based off the Hau mask mold.
In the Blizzard Peaks level, both of the spots where you can use Nuparu's special digging ability are surrounded by a patch of untextured objects. Instead of whatever the developers intended to appear here, there are big, grey-colored rectangles sticking out of the ground.