Continuity mistake: On the skyscraper, when Neo and Trinity kill all of the soldiers, Agent Brown comes to the roof. Neo immediately draws his guns and fires until both of his clips are empty. After that, Neo drops his guns, just as Agent Brown aims at him. During Bullet-Time there are no guns on the floor. When he hits the ground, then the guns are left and right of his legs. (01:41:50)
Continuity mistake: When Anakin attaches 3PO's right eye, one shot has the eye in his left hand, then the angle changes and the eye is being applied with the right hand. (00:37:20)