When Agent Smith is interrogating Neo, after Smith has sealed Neo's mouth shut and he is backed into the corner, when the camera cuts back to Smith you can clearly see a reflection in his glasses of Neo still sitting down in the chair. See more...
Some people have complained that many scenes in the movie have a greenish tint to them. This is deliberate on the part of the filmmakers and is meant to be a clue to the viewer -- all scenes that occur within the Matrix have the green tint overlaying them, while the rest of the movie does not. All scenes in the real world are blue-tinted. See more...
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When Neo is waiting under the bridge to go into the car with Trinity, Switch and Apoc, watch when the car pulls up, you see the back door open completely and then it cuts and then you see Trinity open it again.
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