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Character error 

HAL's verbal description of his chess move (Q-B3), given what he shows on the screen, are from Frank's point of view. This is often regarded as an error, since in descriptive chess notation, the rank is described from the point of view of the player making the move. It should be Q-B6. HAL's errors can be considered either script goofs or clues revealing his internal conflict, since he is supposed to be infallible.
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HAL has apparently forgotten to wish Frank a happy birthday until Frank's parents' video reminds him. This is either a breach in his usual social graces or a lapse in memory. What are the chances that the ship's computer does not have each crewman's date of birth on file?
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Bowman inhales deeply before attempting to re-enter the ship from the pod. Arthur C. Clarke in an interview later noted that this is incorrect. Bowman should have exhaled, as the vacuum of space would have damaged his lungs had they been full of air.
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Continuity 

After Dave Bowman takes his food out of the food slot, two of the containers in his tray exchange positions by themselves. When he first removes the tray, there is a dark red container all the way to the left and a grayish one next to it. When Dave makes his way to the table to eat, the red one and the gray one have switched places.
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When the astronaut leaves the pod to replace the AE-35 unit, he is holding it in his right hand so he can use his left hand to control his thruster backpack. In the next shot showing him maneuvering toward Discovery, the AE-35 is in his left hand.
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The quantity of food changes twice while Bowman and Poole are eating.
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When Dave is showing HAL his sketches, and HAL questions Dave for his crew psychology report: Dave's seating position and the way he holds his sketch pad is not consistent between scenes.
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The phase of the Earth reverses while the moon bus is en-route from Clavius to Tycho.
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In the Pan Am lunar shuttle, we see the Clavius Moon Base approach through the viewing window of the pilot's cockpit in a view like an airplane approach. In the next shot, we see the exterior of the craft, and the cockpit is shown pointing straight up towards the black sky as it lands on the landing gear beneath the craft. It would be impossible for the pilots to view the Clavius approach from the cockpit if landing with reverse thrust engines. All they would see is the sky straight above, and it would be relatively still from their point of view.
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When Bowman is disconnecting HAL in the logic center, he turns a key and a corresponding clear plastic block slides out. However, when he skips the #1 block in one series and turns the key for the high number in the next series, the #1 block in the previous series slides out.
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When the spaceship is docking at the station, the ship and the station are rotating at the same speed as can be seen in the scenes from the ship's point of view. But in the exterior, zoomed out shot of both of them, they are clearly rotating at radically-different speeds.
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When Dr. Floyd has finished flipping through photographs on his way to the TMA-1 moon base, during the cut where he says "Deliberately buried," he is holding a different photograph from the one he is holding in the preceding and succeeding shots.
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In the initial running scene with Dr. Poole on the ship, at the beginning the side with the two occupied long term sleeping units are on his left. In the last shot, they are on his right.
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When Dr. Floyd is giving his speech during the debriefing, his hands are alternately (not) resting on the podium.
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In the first view from the space station looking at the approaching ship, the stars are moving clockwise, so the station must be turning clockwise from the ship's point of view. But in the next shot, the station is turning counter-clockwise from the ship's point of view.
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As Heywood Floyd approaches the Tycho Monolith in the shuttle, the Earth is on the moon's horizon. But a short time later, when Floyd stands at the monolith and it emits its signal, the Earth is directly overhead.
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As Dave Bowman climbs into HAL's logic center to shut him off, the seal on his suit's left hand is broken and the glove separates from the suit (due to the swing). The glove is reattached once he enters the logic center.
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When Dr. Floyd travels to Tycho the speed that the shuttle makes is not continuous. In the shots inside from the cockpit shuttle appears to move real slow whereas outside shots show lot faster speed.
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During the dawn of man, when the ape throws the bone in the air after defeating the rival group, the bone rotates counter clockwise as it goes up, but clockwise as it comes down.
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When Dave goes to climb into the pod the first time, he steps up with his left foot first. When the shot switches to the view on Frank's monitor on the bridge, Dave is climbing in right foot first.
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While Frank is on the tanning bed listening to his parents' birthday greetings there is a cut showing Dave asleep in his 'sleeping pod' that shows the tanning bed at Dave's head, empty.
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The bone Moon-Watcher uses to beat the enemy ape is a femur (upper leg bone), as indicated by the sideways projecting "arm" with a ball at the end. However, the bone shown rotating in the air is a tibia (main bone of the lower leg), as indicated by its blunt ends.
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Errors in geography 

Earth should appear closer to the horizon at Clavius than at Tycho, not vice versa.
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Factual errors 

During Bowman's EVA, stars are moving by, as though the ship was moving at about 5 light years (30 trillion miles) per second. In reality the star field would be stationary. Discovery's velocity of 28 miles per second is insignificant relative to interstellar distances.
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In the first part of the film, when one of the small pod spaceships is landing on the moon, we see dust billowing up from the landing pad. Billowing is caused by the collision of dust and air molecules. But since there is no air on the moon, the dust would not have billowed, and should have been sprayed outward in all directions.
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When the astronauts on the moon are shown walking toward the unearthed sentinel, they are walking normally, as if on earth. The moon's gravity is one-sixth that of earth; hence, they should have appeared to "bounce" a bit when walking, as was seen in the later Apollo moon landings.
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On each of the monolith's first two appearances, the upward camera shot shows the sun/moon or sun/earth in line, artistically above the structure. In both cases, however, it's early morning on earth or the moon, and the sun should actually be on the horizon.
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The spinning pen on the clipper is not spinning around its center of mass: it's spinning about a point well outside its body, which (no matter the mass distribution inside the pen) is impossible.
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Incorrectly regarded as goofs 

When Bowman reenters the ship, he is exposed to vacuum for no more than 10 seconds before operating the repressurization valve. Scientific evidence shows that this would indeed be survivable without grievous harm, notwithstanding the sensational depictions in other movies.
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When Heywood Floyd is talking to his daughter on the picture-phone, she moves slightly out of frame but remains in the shot. Modern cameras can move around to "follow" a person, Stanley Kubrick and Arthur C. Clarke foresaw this.
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HAL 9000 calls his favorite song "Daisy." Although some viewers argue that the correct title is "A Bicycle Built for Two", the 1892 copyright record lists the title as "Daisy Bell."
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The famous centrifuge area of Discovery provides simulated gravity for the crew. However, the pod bay does not rotate, and is gravity-less. Poole and Bowman appear to walk normally there because they are wearing the same "grip shoes" as in other scenes in gravity-less parts of the ship.
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When the hatch is blown with the "explosive bolts", it appears to vanish when it should have been in between Dave and the Discovery, blocking his entrance, However, the door isn't actually detached in this sequence but is, rather, forcibly opened with the door sliding into the side of pod as it normally would, just much quicker due to the explosive bolts being fired.
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When Bowman is carrying out the EVA to replace the AE-35 unit, Discovery's aerial is seen rotating. Normally the aerial is directed to Earth, and unless the ship itself was changing position the aerial would appear stationary. However, the device which controls the positioning mechanisms of the aerial is the AE-35 unit-the unit being replaced. During the time Bowman is exchanging the AE-35s the aerial would have no hardware control, and there is also a small but real possibility that the replacement AE-35 might be faulty. It is reasonable to assume that the aerial would first be rotated to its default position (facing forward, away from Earth) and mechanically locked down until the new AE-35 unit is installed and checked out. The rotation visible in the scene is consistent with that.
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Stanley Kubrick considered shooting the Dawn of man sequence on location in Southern Africa but was unable to due to the expense and also the likelihood of shooting being disrupted by adverse weather. Rear projection as well as colour separation overlay (blue-screen) were considered but not used because both methods would lack visual quality. Instead with assistance from MGM's special effects department the crew developed a new front projection system that used 8x10-inch slides taken on location in Africa. A high-intensity projector was aligned at a perfect angle from the camera and used to project the slide through a partially-transparent mirror that simulated placing the camera and projector in exactly the same place - thus the shadows cast by actors and set objects on the screen were invisible. However the screen material was only available in rolls of limited width and there were variations in reflectivity between rolls. Tearing the material up into small sections and "collaging" them together provided the best uniformity but with effort some variation can be seen in places.
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Revealing mistakes 

On one of the computer monitors in Bowman's pod (visible in the widescreen version only), scratches and a rather obvious film-edit splice can be seen, giving away the fact that the computer graphics are rear-projected film clips. The same scratched-up section of animation is seen in two or three subsequent shots of the pod's control panel.
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As the PanAm shuttle closes in on the space station, the shuttle and station rotate synchronously, so you see the station stay still through the shuttle's windows. However the computer schematic displayed in the cockpit keeps rotating.
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To come up with a convincing effect for the floating pen in the shuttle sequence, Kubrick decided to simply use a pen that was taped to a sheet of glass suspended in front of the camera (in fact, the shuttle attendant can be seen to "pull" the pen off the glass when she takes hold of it). If you watch carefully around the upper left corner of the screen just before she catches the pen, you can see the glass briefly reflecting light as it rotates to give the floating effect to the pen. (On the BluRay release, the sheet is clearly visible through most of the scene. Even swirl marks and what looks like a palm-print can be seen.)
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While Poole and Bowman are watching the BBC 12 interview, the right flat screen is slightly ahead (about two frames). This is due to both screens being rear-projected film clips from two projectors. An actual video feed would be completely synchronized.
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When Dave goes out to repair the AE-35 unit the first time, he parks the pod away from Discovery and rotates it so that the door faces the spacecraft. During the rotation, the lights of the pod reflect on the left side of the screen.
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On the space station, right after Dr. Floyd clears security, and before he meets the Russians, he and another man are strolling along the curved floor of the station. Their bodies' orientation should be radial to the curvature of the floor, appearing to lean forward in the frame, but instead they are perpendicular to the orientation of the frame: they are walking downhill rather that walking along the bottom of the curved floor.
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When the Earth Shuttle stewardess enters the passenger cabin and moves towards Heywood Floyd, she stumbles on the walkway. The nature of the misstep reveals that she is not weightless.
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A weightless environment like the Discovery, which was built in orbit, would have no need for ladders anywhere on the ship other than the centrifuge.
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The people and props in the Clavius meeting hall, and the moon bus to TMA-1, move around and rest in gravity that shows they are on Earth. Moon gravity is 1/6 of Earth's gravity.
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As the moon shuttle lands it kicks up swirling clouds of dust. In the vacuum of space the dust would shoot out straight, as with the real-life Apollo Lunar Modules.
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(At 01:48 - DVD special edition) When Dave is flipping switches in the pod prior to entry through the emergency airlock, his sleeves are hanging from his arms. They should be weightless.
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When astronaut Dave Bowman enters HAL's memory vault, though fully suited up, Dave's left glove is completely detached, plainly revealing his bare arm.
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Although the meeting on the moon is presented indoors, in a shirt-sleeve environment, it is still on the moon. Dr. Floyd walks around the room in full Earth gravity, rather than using the low-gravity "skip" that was adopted by the Apollo astronauts.
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When Dave blows his way into the emergency hatch using the explosive bolts and pressure in the pod, the pod remains static, in reality, the pod would have gone tumbling into space.
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The pacing of the interview on "The World Tonight" is evidently that of an ordinary conversation, not one with 7 minute delays edited out.
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Spoilers 

The goofs below may give away important plot points.

Continuity 

At the end of the film, Dave uses the last remaining pod to get a closer look at the huge monolith. The hangar bay door that opens is the one in the center. The center bay was from the pod that killed Frank and was drifted into space. The bay door to the left (outside perspective, looking at the Discovery) was from the pod Dave used to retrieve Frank's body. The pod became useless upon explosive re-entry of Dave in the Discovery, so the only left pod should be the one at the right bay door and not the center door.
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Continuity 

While Dave gets outside the Discovery in attempt to retrieve Frank's body, HAL kills the hibernating crew, a shoot of the hangar bay shows the door to the left open. When Dave is back in the Discovery and away to shut down HAL, the same door is closed.
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