(at around 18 mins) When Lindsay spills her drugged glass of water, it is nearly empty, and approximately 3/4 of an inch (one centimeter) of liquid remains. In the next scene, after Dr. Heiter goes downstairs and the woman says, "It's freaking me out!" the glass is half-filled with water again.
(at around 50 mins) When the doctor joins the three for the first time and begins taking photos, he is using a Canon Digital Rebel. When the camera angle changes and shows him taking photographs again, he is shown to be using a Nikon camera.
(at around 1h 17 mins) While the captives climb the spiral staircase, they are bleeding and pools of blood can be seen on many of the steps. However, a moment later when the camera shows a shot of Dr. Heiter at the top of the stairs looking down the hallway by the bedroom, there is not a drop of blood on the floor where the three had crawled.
(at around 33 mins) When Lindsay is running up the stairs with a bloody arm, she grabs onto a corner of the wall, but the blood was there before she touched it.
(at around 37 mins) When Lindsay is in the pool her hairstyle changes between shots.
(at around 1h 2 mins) The phones in the house are not real phones, but they are connected to the doorbell as an intercom system. This is shown when Dr. Heiter answers the intercom, and it is the police at the door.
(at around 26 mins) When Dr. Heiter is taking an unconscious Katsuro out of his car, you see Katsuro "help" Heiter by putting his right arm on the door frame to push himself up, so Heiter can carry him.
(at around 5 mins) When the two girls realize they're lost in the woods, there are two scenes where the video is mirrored. This is evident from the car registration plates and the driver's seat which is on the right.
(at around 53 mins) When the human centipede is being trained to fetch the newspaper, Lindsay can be seen flexing and extending her legs despite having the tendons of her knee cut to prevent this.
Though possible, the ingestion of human excrement would most likely have cause the individual to throw up, thus leading to the individual's demise as they would choke on their own vomit and the excrement.
Whenever Dr. Heiter walks in the room where his patients lie down, a breathing machine can be heard. However, none of the people are connected to a breathing machine with tubes, so this sound doesn't make sense.
(at around 33 mins) When Lindsay is hiding in the doctor's bedroom and screams, "You're a sick man; you need help!" you can see a face move in the mirror behind her (which is definitely not hers because of the hair).
(at around 47 mins) When the new glass panel is being put into place, the camera crew and equipment is clearly visible.