Corrected entry: This happens during the scene when Morpheus cuts "The Twins" car with a sword, and shoots it. Watch how close Morpheus is to the car when he shoots, then when it explodes look around on the ground. There is a wide angle camera shot, and Morpheus is not there any more, even though he was about 10 feet from the car. Then when the shot goes to a higher angle, Morpheus reappears. He also looks transparent and 2D in some of the higher shots of the road.
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Correction: You actually do see him. When the car explodes you see Morpheus at the left side of the screen. Probably only visible in widescreen.