When Morpheus shows Neo the agent training simulation, the girl in red turns into an agent. When they pause the simulation you can see the reflection of Neo with a gun pointed at his head in Morpheus' glasses. When you look in one shot there is a visible white line/mark (scenery?) between the gun and Neo, in the next shot it is gone and then right at the end in the final shot it's back again. See more...
When Neo is at work in his supervisor's office getting yelled at, notice the window washers. When the camera shoots from the outside of the building, look at the soap on the window.. it strangely resembles the Matrix pattern as displayed on a computer screen. Also take notice of the look of confusion on Neo's face - like he had seen that pattern somewhere before. See more...
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When Neo is going to open the door to enter the Oracle's house, you can clearly see a camera on the doorknob. There's a sheet over it painted to look like the wall behind it, with a representation of Morpheus' tie too, because he's blocked by the camera.
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