Audio problem: On the freeway when the Twin stops firing when the car goes behind a truck (shortly before he floats into the car), you can hear about 5 shots being fired by him after the muzzle flashes stop and the gun stops shaking. (01:22:15)
Audio problem: When Neo, Morpheus, and Trinity are meeting the Merovingian, he starts talking about French wine and the language. When the shot changes to behind the Merovingian, he is seen talking, but his mouth never comes close to the words we hear. (01:01:55)
Audio problem: After the Keymaker has been shot, Morpheus and Neo rush to him and turn him over. The Keymaker's gasping for air is very audible, but the first reflection of him that we see in Morpheus's sunglasses shows that his mouth is tightly closed. This is only visible in that one reflection shot. (01:49:00)
Answer: This was made just for the trailers. The same part (without the Matrix code) can be seen when Smith says "suprised to see me?" to which Neo replies "No." and puts on his sunglasses before the Burly Brawl.