In the beginning of the movie, Malcolm is seen putting on Aqua Blue sneakers (Air Jordan 3) but when he is on his bike in the following scene, his shoes are White and Red. In the next shot, they are back to the Aqua Blue version.
At around 20 minutes, when Malcolm is at Dom's birthday party, when he sees Nakia through the crowd holding a champagne flute. Malcolm is shown wearing his golden necklace above his denim shirt, then the camera quickly switches between Malcolm and his friends as he approaches Nakia, and the necklace changes position from above to under the denim shirt.
When the film shows us Tony Johnson, who was killed accidentally in a shooting at a fast food restaurant, he is playing a Game Boy, and the narrator tells us he was "seconds away from defeating Ganon" who is the recurring antagonist of the Legend of Zelda series. However, the only Legend of Zelda game available on the original Game Boy was Link's Awakening, which does not feature Ganon.
While the camera focuses on Malcolm talking to Lily in the hallway of her father's house, the cinematographer is reflected in a framed picture on the wall.
Malcolm ends his Harvard application essay, asking if they would ask a white kid why they want to go to Harvard, suggesting they wouldn't. As this was an application question, obviously they ask everyone that question.