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Anachronisms 

The 1997 Pathfinder/Sojourner is labeled "UISA", like the crew's 2052 equipment. The Pathfinder/Sojourner was launched by NASA, and included the US flag and the Jet Propulsion Laboratory logos.
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Character error 

The creatures on Mars are called nematodes, which are unsegmented worms. With jointed exoskeletons and paired legs and arms, the creatures resemble arthropods.
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Burchenal says he is an expert in genetics, yet he refers to the 4 DNA nucleotides as A, G, T and P. They're actually A, C, G, and T. It's corrected in the German dubbed version.
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In the orbiter, as Bowman restores power and oxygen, and tries to restore communications, she flips through a bunch of switches in rapid succession. One switch breaks off and falls.
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Bowman says it will take 40 minutes for Houston to reply. The signal travels at the speed of light, but the distance from Mars to Earth varies. On Feb. 5, 2057, it would take 5.7 minutes to reach Earth, which means an 11.4 minute response time (not including time for Houston to formulate a reply).
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Gallagher tells Bowman that she can't stay in orbit around Mars without burning more fuel. Once in orbit, past Mars' gravitational field, they would only burn fuel to change orbit.
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When Bowman has reanimated Gallagher, the ship's computer tells her to "stand him up." Gravity isn't restored yet, so there is no "up".
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When Burchenal explains that humans have killed all frogs on Earth, he mentions that they have become extinct because they could not breathe through their skin anymore. Yet, the recent declines in frogs population are also likely to come from diseases, habitat destruction and climate change. The decreasing of the ozone layer is also supposed to play an important part in these declines.
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Continuity 

The physical configuration of Mars-1 changes throughout the film. In some shots, the MEV is docked at the front of the spacecraft. In other shots, the MEV dock is empty before launch.
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Errors in geography 

The two moons of Mars, Deimos and Phobos, are so small that they don't block enough light to cast shadows on the Martian surface.
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FLIPPED SHOT: During the opening credits, as "Warner Bros. Pictures" is displayed on the screen, Earth is in the background, with the US east coast (including a reversed outline of Florida) on the left of the screen. As the camera pulls back, the US west coast is on the right side of the screen. In the following shot, when the international space station is shown with a shuttle approaching, the US coastline is correct.
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Factual errors 

Gravity on Mars is much weaker than shown in the film.
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While orbiting Mars, the orbiter would be in darkness for a few hours, not the entire Martian night.
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Incorrectly regarded as goofs 

After the ground crew crashes on Mars, sunrise clearly shows the sun in a blue sky, despite the lack of water on Mars. The color of the sky is an atmospheric effect (blue light scatters more than red or green), and has nothing to do with nearby bodies of water.
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Plot holes 

After Gallagher retrieves the radio from Pettengill, he tries calling Bowman with no result. He says Mars 1 may still be on the night side of Mars. It is clearly night, so Mars 1 should be in range.
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Mars lost its magnetosphere several billion years ago, allowing radiation to react more strongly with the Martian ionosphere and keeping the atmosphere too thin to support human life. This is due mainly to the cooling off of the Martian core, whose magnetic field supports atmospheric retention. Using algae to re-oxygenate the planet would be futile; the atmosphere is too thin to keep the oxygen from escaping into space.
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Revealing mistakes 

During the ice storm on Mars, no one's breath is visible on the ground, despite sub-freezing temperatures.
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The Russian text in KOSMOS launch ship computer menu is just a random set of symbols.
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Spoilers 

The goofs below may give away important plot points.

Continuity 

In the closing shot of the Mars orbiter returning to earth, the Mars lander can be seen on the nose of the ship.
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Continuity 

After Pettengill escapes with the radio, and Aimee kills him, Pettengill's green beacon is shining from his body past his feet. When Burchenal and Gallagher arrive at Pettengill's position, the green beacon is pointing past his head.
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Plot holes 

The nematodes eat the algae which was sent from Earth. If they are the only life on Mars (no other forms are shown or mentioned) then what did they eat to survive before Earth began sending it?
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Revealing mistakes 

When Lt. Ted Santen and Chip Pettengill are arguing near the cliff, 3 holes are visible in the chin area of their 'air-tight' helmets.
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