116. Magic Folder
Look closely at the folder Agent Smith is playing with. In the first shot, he hasn't turned any pages over but in the next shot, he has. How did he do it so quickly?
115. Smith's Moving Glasses
Things moving by themselves are quite common in the Matrix. Agent Smith takes off his glasses and puts them next to him. When he goes to put them on, they have moved half a meter across the table.
114: Why Not Godzilla?
And is there any reason the agents have to look like they do? The machines control The Matrix so they could make what ever creature thing they want to get Neo and the gang. Why not a giant lizard with 50 arms that breaths fire? Or why not make them look like one of the normal humans instead of stereotypical FBI agents?
113.No One Puts Neo In the Corner
Reflective surfaces are always a pain in the butt for filmmakers and editors. There is always the danger that the flow of the film will be interrupted by a reversed image of the cameraman ruining the shot. It can also screw with continuity as it did here when Agent Smith is interrogating Neo for the first time. When Neo is huddled in the corner with his mouth sealed up, the close up of Smith's glasses shows Neo still sitting in the chair.