Continuity mistake: Simon Phoenix's eyes change. Sometimes the blue is in the left eye, sometimes in the right.
Other mistake: The Verbal Morality Code seems to be applied in an almost haphazard fashion. Several times throughout the movie, both Spartan and Phoenix swear, and do so near an area where they should be vocally reminded of breaking the code, in fact have been previously reminded, and in spite of them not moving from that location are not warned again in the face of repeated swearing.
Answer: I'm assuming you're referring to when Simon says "Damn, I'm possessed!" He was hacking the machine when he said it, perhaps he'd corrupted the program or shut off the microphone as a side effect?
Grumpy Scot