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.
Revealing mistake: In the freeway chase scene, look carefully at the interior of the cars that get flipped over by the Agents and the Twins. All of them are completely empty, meaning that either they are remotely controlled or they are simply towed by a hidden vehicle. This is most obvious when they are flipping in slow-motion.