Neo's 9mm machine gun drops .223 cartridges during the shoot-em-up scene.

When Agent Smith shoots Neo in chest the first time and you see the spent shell hitting the ground, the end is smooth, but when it shows the gun from above you can see that they are blanks with crimped ends not the smooth edge like a real bullet.

When Neo is in his work place and receives a FedEx parcel containing the phone, a close shot of him shows him about to rip the parcel open, the next shot from far away shows him with the parcel at his waist picking it up then opening it.

There are two occasions when you can see boom mikes reflected in a character's sunglasses when looking up. One when Morpheus is explaing to Neo what the Matrix is when he look up as he says, "Fate as it seems is not without a sense of irony." And in the end after Neo makes the phone call in the booth, right before he "flies".

In the subway fight when the agent punches at Neo but Neo pulls back and the agent punches through the cement pillar you can easily see the weak/soft part were he is supposed to punch through.

Beginning of the movie - Trinity is running away from Agents et al., and crashes through the window, rolls down the stairs. When she looks back, the light she smacked is swinging and squeeking. A second later it is dead still. But still squeeking.

When Neo is on top of the building looking down at the cars all the traffic arrows drawn onto the roads are pointing in the opposite direction that the cars are traveling (some the movie was shot in Sydney, Australia all their cars drive on the left hand side).

In the rooftop scene where Neo is dodging bullets, he drops his guns on the floor, then the agent starts shooting at him and the camera travels around Neo and the guns are gone! And then they are back when the bullets time effect is over.

Before Agent Smith shots Neo at the end of the movie there is a large bloody mark on the back wall to Neo's right. This was left by mistake from the previous take. Watch when Neo falls back, sure enough, he hits his mark perfectly.

When Neo falls out of the water slide if you slow it down he has on a orange life presever on his neck.

After Neo is done visiting the oracle, she hands him a cookie, to which Neo takes a bite of the cookie. In the next shot he is trying to figure out why he isn't the one. He talks to Morpheus and the cookie in his hand is a whole cookie, no bite in it at all. Then the shot after that there is another bite.

When Morpheus is talking with Neo, many mistakes are made as angles are cut. For example the pills jump hands, or one scene Morpheus has pills, another he doesn't, or his hand jumps locations although the speech implies time is traveling normally. Also Morpheus's belt changes.

In the subway scene, after Neo and agent smith have emptied their clips and fallen on the ground, agent smith tosses his gun away while they are both on the ground, when they are shown standing up, you'll see agent smith tossing his same gun again.

At the end when Neo is being shot in the hallway, look closely at the ceiling. Note that there is nothing hanging from the ceiling. Later, when Neo gets up, and starts fighting the agent, if you look at the ceiling then, you see a bunch of wires and crap hanging from the ceiling.

When Keanu Reeves(Neo) walks into his work building, there is a sign on the building the says Metavortex, or something like that. When Neo leaves the building the sign now says Metavortech.

I am not sure if all of these are valid, I found them around the web. If you have any more, or want to discuss these "Glitches", go to the forum! :)