In the last scenes where Neo is shot by the agent, Neo is shot once, checks himslef for blood and then is shot again. He falls to the wall and you see two bullet wounds.

The screen the changes and Neo is shot at least seven more times, and yet the agents choose to use the most powerful clip gun in the world a Desert Eagle probably .375 or maybe the .50EA version. This presents a few problems;

1) Desert Eagle can only hold 7 bullets in a normal clip. The agents do not have clip extensions and so are cheating then.

2) Neo is shot roughly 9 times with a D.E, this poses a small problem as there are only 4 bullet entry wounds.

3) A D.E at short range would have gone through him and straight into the opposite wall, this would have made a cricket/baseball sized hole in his back.

There are a few more of these clip problems ill point out ;

During the Lobby shot out one of the guards dives in front of another and radios for help. The camera is at an angle so that you can see the bullet hole appearing the the geezer behind him just where he was diving. So the bullets went through him!

In the Lobby again Neo fires about 7 shots a piece from his dual berrettas, I thought berrettas had large clips of 15!

On the roof the agent and neo are hooting each other, neo shoots first with 2 Barrettas (Wep of choice i guess) and he fires about 10-12 shots, u see the guns have still got ammo in and he throws them down, the agent the shoots 7 times at neo and walks over to him, says the quote "Only Human" and goes to shoot him with an empty gun, but strange he must have reloaded in fast motion!!