Continuity mistake: In the scene where the police car is chasing Ben Affleck and Uma Thurman on a bike down in a tunnel, in one shot, the police car's flashing light on top is ripped off by the low ceiling. In the very next shot, the lights are still on the top. The next shot shows the lights are gone. (01:13:50)
Continuity mistake: Towards the end of the movie, when Michael and Rachel split up between the glass door, her left hand is cut and bloody, then it is not, then it is again, as it is pressed against the glass. (01:37:35)
Revealing mistake: In one of the shots of a newspaper you see a serious grammatical error for a headline. The use of "it's" instead of "its". It was something to the effect of "Ahead of it's Time". Forgivable for a note left by a character, but a mistake that real newspapers just don't make. Just FYI: The actual headline is "Nexim Announces It's Answer to ARC's Living Display". (00:11:40)
Answer: He does recognize Rachel from the party as well as when he when he saw her at Allcom. The only things he doesn't remember are the last three years of his life since starting the project. So, while he does remember her, the three years they spent together while at Allcom are a total blank. This recognition is shown when he meets with Porter who helps him escape.
But later, when he is going through her stuff, he says he doesn't remember her. Also, if he did remember her, he would have known it wasn't her when the imposter was in the restaurant (also no need to have the imposter try to dress like her either).