At the conference near the end, when Dr. Larry Roberts is disguised as a security guard, during several sequences getting in and out of elevators the wound on the side of his mouth disappears and reappears.
When Dr. Roberts is looking for a hiding place for the key card, the clock on his bookshelf indicates that the time is 2.30. Seconds later, it has jumped forward 15 minutes, showing 2.45. We know this is before he's been hypnotized because the negative effect hasn't been used yet and the background music has been playing continuously.
Susan Dey's hairstyle changes drastically when Cindy visits her parents; it has much more curl than it does in the rest of the film.
Near the beginning, Lisa the model is shot by the LOOKER gun while in her doorway. She recovers and as she walks into the bedroom there is nothing on the bed. She opens the closet door and picks up the dog, and as she turns around the case for the gun is now on the bed. She was not shot again until after she left the bedroom.
As Cindy is being scanned, she's cautioned about moving her jaw because she's talking. Immediately after that, she raises her head to look upward without a warning about it.
During a car chase, Dr. Roberts gets hypnotized by the Looker gun. When he comes to, his car is in the fountain, with the well base being significantly taller than the clearance height of his car and no obvious damage to either the car or the fountain.
During her visit to Larry's office, Lisa states that she is not 'perfect', listing her 'defects' down to the millimeter, ending with 'I have a mole on my ribs'. The doctor agrees to make the changes. Cindy also had surgery by Larry to make her 'perfect'. However, during Cindy's volleyball photo shoot it is very apparent that she has two moles on her chest/shoulder area and what looks like a sizable wart between her stomach and breast bone. Perhaps "one" mole may be properly placed according to the computer models they used, but two moles and a wart, especially in their positions, is highly unlikely.
Arriving at the scene of murder #3, the doctor pulls up to the apt building and looking up at the balcony, he recognizes which apartment is the murder victim's after reporting to police that he'd never been social with his clients and could not possibly be able to guess which apartment it was.
Lieutenant Masters arrives on the scene where the model has fallen from the balcony. His car's tires squeal to a halt, yet we see that his car pulls to a normal stop.
At precisely 4:50 (DVD timing), when the model opens her apartment door and her dog barks, you can clearly see the trainer's hand motioning for the dog to turn around (lower right hand corner of the screen).
At 11:30, a boom mic is reflected in the artwork on the wall, behind Dr. Roberts.