Corrected entry: Revolving bullet-time scene with Neo and Agent Smith in the train station. Note the speed they are turning and that of the bullets leaving the gun is identical. This would imply when played in 'real-time' they are moving at the same velocity of the bullets. The bullets should (obviously) be moving at a faster speed.
Corrected entry: Fact 1: Anyone who is still a part of the Matrix is a potential host for an Agent. Fact 2: Agents can see though the eyes of any "matrixed" human (ex. Agent Smith saw what the subway bum saw). Fact 3: The Agents knew that Morpheus would contact Neo. Taking these facts into consideration, why did the Agents have to plant a homing bug on Neo? They knew that Morpheus wanted to contact Neo so why not just monitor everything that Neo saw, wait until he met up with Morpheus and then take over Neo's body and grab Morpheus for questioning.
Corrected entry: When Neo is being brought out of his workplace by the agents, there are the three agents walking with him. However, when they show the scene in the side mirror of Trinity's bike, Agent Smith cannot be seen but the other two agents can (you can see it if you freezeframe the DVD). (00:16:05)
Corrected entry: If the machines know about the Human Resistance, why, oh why do they not kill humans that awaken rather than let them fall down the drain?
Corrected entry: Morpheus tells Neo that they don't release people after a certain age, but he did it because Neo is the one. However, later we find out that Cypher has been out of the Matrix for 9 years. This is hard to understand because Cypher is at least 10 years older than Neo. Why then did they release Cypher, if he also was past the certain age?
Corrected entry: If the agents can jump into the body of anyone in the Matrix, why didn't Agent Smith jump into the body of one of the cops who try to capture Trinity at the start? He is told there are cops up there before she takes them out, if he had jumped straight away he would have had her trapped.