Minor Plot hole: Trinity sneaks up on an Agent right before he kills Neo on top of a building and proceeds to say:
Trinity: Dodge this !
Agent: Thank you Trinity. Having the power to dodge every handgun bullet I know is coming towards me, your notification of an impending projectile to my head was appreciated although not necessary since you touched my head with the tip of your weapon before uttering your arrogant one-liner. If we followed the premise of my powers to the letter, I would easily ‘’Dodge this’’ without breaking a sweat, not only because I don’t and can’t sweat but precisely because I know when you will pull the trigger and with the exact angle. But since you both have to survive this scene in order for the movie to continue, please allow me to do jackshit and eat your bullet in my cyber-brain. Adieu.
Minor Plot hole: In the intro, when Trinity is on her way to escape the Matrix, Agent Smith decides to slowly ram a truck in the phone booth instead of shooting the phone off or Trinity with his gun. Agent Smith later does exactly this thing when he shoots off the phone so that Neo can’t escape the Matrix – why didn’t he do it then ?
Minor Plot hole: Agents in the Matrix can take control of anybody that is still connected to the Matrix. There are everyone and they are no one ! But since we only learn of this as an audience midway through the film, the agents do not show this power before that when they could have taken control of the police officers in the first scene when Trinity was cornered. Otherwise she would have died.
Major Plot hole: After Morpheus is saved and safely back in the real world, Trinity decides to open her heart to Neo in a dirty metro station because it is much more important than everything else right now. How retarded do you have to be to not realize that all those things you want to say can be said a few seconds later in a safer environment where three deadly invincible agents are not swiftly searching for you? Trinity, in a matter of seconds, went from a tough logical badass to a stupid emotional meat-bag. God I wish Smith shot her good.
Major Plot hole: After the delicious sex scene between the lobster and Keanu Reeve’s bellybutton, Morpheus calls Neo; tells him the phone is tapped……..and tells him where to go to meet Trinity. So far, it's kinda stupid. 1-0 for the Machines. But when Neo meets Trinity under the Adams Saint bridge, no agents are there. If they all heard where Neo was going, how hard could it be for a single agent to take control of one of the citizens living a few feet away from the bridge ? Was their Google map server down ? 1-1 for the draw.
Super Plot hole: The machines no longer have the sun to harness most of the energy they need to survive. Their plan is to use mammals and harness their heat to survive. Excluding the fact that it rapes the second law of thermodynamics (being part of the premise of the movie this can be excused) the real problem with the screenplay is the machine’s decision to use humans. If they are only interested in body heat why not use cows? They would give similar amounts of heat and as a bonus…..you don’t have to create a complex dream world for them to live in because they won’t give a shit – they're cows.
Plot contrivance: Morpheus is shot in the leg by Agent Smith when he is reaching for the helicopter. The damage to his leg is big enough to make it impossible for him to continue running and he has to jump for Neo to catch him. A mere 60 seconds later, he stands and run with Neo and Trinity without any problems because he can play with the design of the matrix to convince himself he is Wolverine.
Unaddressed Issue: Why are agents looking the way they look? Wouldn’t it be much more effective to let the agents take control of the bodies they want and keep their physical appearances? It’s an important issue to put on the table since absolutely nothing from the movie indicates it would be a difficulty for the machines to make their agents more suitable to catch their prey.
Unaddressed Issue: When people wake-up from the Matrix, why can't the machines simply kill them? You might say that they think they kill them by flushing them down in the sewers, but since all those red pill takers end up reconnecting in the Matrix to free more people, they can simply see with their own robotic eyes that they never died. Let this be clear, the machines know that once in a while, humans wake-up: it’s in the design of the Matrix. But most of their problems would be over if they simply killed every human who wakes up. Shouldn't be hard to send a few shots of electricity in those pods full of pink liquids.
Unaddressed Issue: How does Cypher pull-off his stunt to make a deal with the machines? His meeting with Agent Smith to discuss the formalities of his reintegration was inside the Matrix. But every time someone is in the Matrix, Tank the operator is there looking at the codes and he would have known that Cypher was having dinner with Agent Smith. However, the movie implies he went in the Matrix alone – but it goes against everything that was shown in the movie, that is, no one can connect himself in the matrix without help. Did he learn to connect himself alone? Was his mustache long enough to use the interface of the chairs and start the coitus between his head and the big metal rods?