(at around 1h 22 mins) After Peter revives from entering into the subconscious, he tries to sit up and raises his hand to his face to remove the cloth, but in the next shot his hand is on his chest. When he does take the cloth off his face he places it at his left side. In the next shot, the cloth is moved to right under his chin.
(at around 14 mins) When Catherine is at home, the TV in the background is playing Fantastic Planet (1973). Scenes from the movie are shown out of order and the soundtrack does not match what is being shown.
(at around 49 mins) Just before water pours on Julie, the monitors around the room show her eating (at least, holding food). But when the camera cuts straight to her, she isn't holding anything (error caused by deleted material).
(at around 1h 3 mins) Carl's first victim is sitting up with her breasts partially covered by bloody water; in subsequent shots, the water is higher on her body from the actress sliding deeper in the bathtub as seen by the angle of her head on the edge of the tub.
Toward the end of the movie, the two FBI agents are seen going into and flying in the helicopter, but in the next scene, they are seen in the laboratory to witness the final experiment.
An albino dog would lack almost all color. Pink nose & eyes, not blue eyes & black nose.
While the killer is washing the dead woman's body, her nipples are clearly seen and they are erect. Nipples only become that stiff and erect as a response to stimuli which is impossible if the body is dead.
Any goofs occurring in the "subconscious" world which the characters enter, do not have to be consistent or conform to realistic physics, as the subconscious is arbitrary, and can create whatever rules it wants.
The cell contains a toilet that would ordinarily act as a drain, but presumably Carl has arranged for it to close when the cell is filling with water.
(at around 25 mins) The plane they take to the city where the killer lives is a jet (with jet engines). A plane with propellers is visible when they get off, but this is a different plane.
(at around 21 mins) When Julia gets into her car in the parking garage, she backs up and is tricked by Valentine's ploy to lure her out of the car. She has to back up, because there is a barrier in front of her car.
(at around 1h 9 mins) The gemstone on Julia Hickson's engagement ring is tucked under her hand when she is looking for loose fits, thus making it appear to be a wedding band (though she isn't married yet). The stone is visible when she yanks on the pipe.
When Catherine is at home and looks at the newspaper clippings on the wall, one of them is about Edward. It contains many grammatical and syntax errors that no newspaper would ever allow to be published.
(at around 1h 9 mins) During the second filling of the cell the cameraman, and possibly the director (another person is seen next to the cameraman), can be seen in a reflection on the inside of the cell. When the camera pans to the left as Julia pounds on the glass walls and curses out her captor, you can see two figures (one with a camera) reflected in the glass.
Catherine finds herself in a dream world version of the lab when entering Carl's mind a third time, but since he never saw this facility before he was wheeled into it, and he was comatose at that, how would he have any memories of this location imprinted in his mind? Though logic does not operate in the dream world, and nothing has to make sense, it still begs the question of why he would have memories of a place he never visited while conscious.
It would have been simpler and quicker for the FBI and police to find an electronics expert to trace the video feed, be it radio broadcast or hard wired, to find Julia Hickson.
Though Catherine will not face any consequences for "killing" Carl in the dream world, as there's no way anybody can prove that she did (as he simply died suddenly while comatose), and she wouldn't even have to use the self-defense excuse, she still does not seem to suffer any consequences for changing the password to the lab's security door and forcefully using the equipment to enter the dream world without the consent of the scientists.
(at around 32 mins) Though "Whalen's Infraction," a brain disorder which is said to have accelerated Stargher's schizophrenia was made up for the movie, an infraction actually refers to an incomplete bone fraction and affects bony tissues, not the brain. Cerebral infarction ("infarct" instead of "infract"), or tissue death due to lack of blood flow, does occur in the brain, but this is said to cause schizophrenia-like symptoms and would not cause or affect schizophrenia itself.
In the movie, the cops are looking for the breeder of the killer's dog, which they say is an albino German Shepherd, when in fact, the dog in the movie is an albino Siberian Husky. Note the blue eyes in the film that the dog has.
Peter wastes precious time telling Catherine his past as a criminal defense lawyer outside of the institute, when (according to his own words) time is running out to find Julia before she drowns in the water tank.