Revealing mistake: When the Key-Maker shuts the door in the corridor-scene while being shot at by Smiths, one dead Smith-body lies in the corridor, the one that Neo knocked through the crown of other Smiths. When you look closely at the body of the Smith, you can see his right foot slowly moving.
Suggested correction: Who says he's dead? It just got knocked down.
Continuity mistake: In the freeway chase, Agent Johnson jumps from an overpass onto the top of the truck carrying Morpheus and the Keymaker. Just before the truck goes beneath the overpass, a freeway distances sign (Whipple Ave ½, Woodside Rd 1-½, Marsh Road 3-¾) is briefly visible. As the truck emerges on the other side, the same sign appears again, behind Johnson, to the right.
Revealing mistake: During the car chase scene 1 of the twins shoots through a car window causing it to flip. If you look closely you can see the stuntman wearing his helmet. (01:25:55)
Continuity mistake: On the highway, while Trinity jumps from the trailer on the motorbike, the sun changes between shots.