Audio problem: When Michael is forced to do "errands" for Brennen, they stop by Jonathan Carver's house to get numbers from him for a voice key. The code played back at the facility is 71348. He says "3" in a medium pitch (tone) at the house, but it is high pitched when played back at the facility; he says "8" in a medium pitch, and it's also high pitched later. And finally he says "9" in a low pitch and it's played back medium pitch. Also very obvious is the fact that Jonathan never says "1" or "7."
Audio problem: Despite extensive overdubbing in the scene where Bob returns, the roar of helicopters can still be heard in the background. According to producers on the DVD commentary, the noise was due to firefighting aircraft overflying the sound stage during devastating L.A. brush fires in the Fall of '06. (00:25:30)