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Audio/visual unsynchronised 

When the Golden Gate Bridge is melting away, one of the main support wires whips back and slams into the car of the guy whose arm was burnt. The audio has him screaming, but if you look in the rear-view mirror, you can see that his mouth is only partially open in the same expression of confusion he had seconds before.
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Character error 

When Rat offers to help Josh stop Project Destiny, he tells Josh "here is the information you're primed for". Josh understands the code and enters "prime numbers" into his computer: 1, 2, 3, 5, 7, 11, etc. But 1 is not a prime number. (Note: 1 used to be considered prime number, but modern number theory doesn't think so - Josh ought to be up to date with these things.)
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A display inside the ship misspells "integrity" as "intregrity".
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Dr. Zimsky states that he chose the Marianas Trench as the launch location because the crust is thinner there. The Marianas Trench is a subduction zone, where the Pacific plate is being pushed under the Philippine plate. Large amounts of sediments are built up at subduction zones as one plate scrapes the top off the other plate, so the oceanic crust is actually a good bit thicker at the trench. A better location would have been in the middle of a plate, such as near Hawaii.
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While Rat is looking up Project DESTINI (Deep Earth Seismic Trigger INItiative), he types Project Destiny instead of using the proper acronym.
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In the scene where Rat is being recruited, he uses a whistle to hack Josh's cell phone, telling him he now has "free long distance for life." However, by the time the movie takes place, not only were all land-line telephone trunk exchanges digital (meaning that temporary free long distance could not accomplished using a 2600 Hertz tone), but any cell phone exchange would be exclusively digital and therefore would not utilize tones as signals to (mechanical) trunk lines. Also, the whistle Rat uses is far lower in pitch than the necessary 2600 Hz.
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Continuity 

While on the ship at sea looking for Josh and Beck, Rat's hair seems to grow shorter. When Rat is talking with the general inside, his hair is normal length, but when he runs to alert the general about the ultrasonics, his hair is at least an inch shorter.
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During the space shuttle crash, when Rebecca is trying to find an alternate landing site, the writing on the maps disappears in the next shot.
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When Zimsky is explaining what destiny is all about, he spells out the project name as an acronym of 'DESTINI', but just two minutes later, and a number of times after, the text that comes up on screen, over a shot of the fictitious location, clearly spells it out as 'DESTINY'.
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During the "pigeon stampede" the taxi windshield is cracked when a pigeon hits it. This causes the driver to swerve onto the sidewalk. Then cut to another angle and as it drives up on the sidewalk, the windshield is no longer cracked.
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When Josh is preparing the last compartment to be ejected, he brings in the fuel rod, sets the timer, and manually ejects the compartment. But, Josh never pulls out the trigger within the bomb after he sets the timer.
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In the first shot of the space shuttle orbiter, it is labeled the Enterprise, an orbiter mockup built for early approach and landing tests that could never actually be launched into orbit. In communications the orbiter is identified as the Endeavour, and it bears Endeavor markings once it lands on Earth.
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Errors in geography 

When the crew approaches the launch site where they will descend to the Earth's core, a caption reads, "Marianas Trench - South Pacific". The Marianas Trench is in the North Pacific, east of the Philippines.
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They fly in over Dodger stadium, heading south. Endeavour ends up with sun shining on its port side, indicating it's nose is pointed north. The 6th street Bridge (with double steel arch) behind it could not be behind the aircraft because they showed multiple shots of gliding over it as they headed south.
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Factual errors 

There is no direct power link from the lower 48 to Alaska. The Continental electrical grid extends up to northern British Columbia, then stops. The Yukon (which actually is between BC and Alaska) is not "tied in to the grid", so therefore it would be impossible for them to "draw power from the rest of the US", which is silly anyway, because all the power they were drawing would actually have to go through Canadian power lines.
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When Rat is trying to "hack" his way into the DoE's "Intranet Database", on his first try to access a file he gets an error "404 - Access Denied". Actually, web server error message 404 corresponds to "File Not Found", while 403 is "Forbidden / Access Denied". Since Rat is working from a seemingly secured computer - he seems to have no trouble at all accessing the DoE's "Intranet" as clearly stated on the screen - probably the correct error message should have been "401 - Unauthorized".
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When the space shuttle has to make the emergency landing at the beginning of the film, it retracts its landing gear to fit under a bridge. However, in order to save on weight, the space shuttle landing gear does not have the necessary machinery to retract its landing gear; the gear must be manually returned to its stowed position.
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After Virgil is launched it is accompanied for a short time by humpback whales that sing to it. Humpback whales do not swim at 800ft beneath the surface.
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When Virgil first enters free-fall after drilling into the empty space, the characters are all thrust forward in the direction of the fall. Actually since they are in free-fall, they should suddenly become weightless in the cabin as they would fall at the exact same rate as Virgil.
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When the shuttle's landing gear is deployed during its emergency landing, two buttons are pressed; the first one is labeled "ARM". There is nothing to arm with respect to the orbiter's undercarriage. The deploy mechanism simply opens the doors and allows the undercarriage to swing down by gravity.
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As a body enters the interior of a large mass, such as the Earth or any other planet, the force of gravity begins to decrease at a linear rate, and reaches zero at the center of the planet. Although the ship is hovering above the inner core, and is therefore not at the exact center of the earth, the gravitational force would be nearly zero, so the actors should be able to float around the ship as if in orbit. As is, they walk around as if under the influence of normal gravity experienced on the surface of the Earth.
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While birds do indeed make use of the Earth's magnetic field for navigation during long-distance migration, when flying short distances they will rely on their vision. A disturbance in the magnetic field would have had no impact on the pigeons' ability to see - and thus avoid - obstacles in their path.
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Hawaii is in the middle of the Pacific tectonic plate, not in an area between two plates as in the movie.
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The entire space shuttle landing sequence has been time-compressed to just a couple of minutes. In reality it takes about half an hour, with many maneuvers taking place during reentry to bleed off speed. At no time is the shuttle depending on the Earth's magnetic field to navigate. The shuttle uses inertial navigation systems and GPS to keep track of its own position. NASA also has tracking stations on the ground doing the same. These things combined means the notion that the shuttle would suddenly and unnoticed turn up that much off course and off altitude is not plausible.
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Miscellaneous 

In the credits, Bruce Greenwood's character is listed as "Richard Iverson" when he was actually "Robert Iverson" and frequently referred to as Bob throughout the entire film.
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Incorrectly regarded as goofs 

At about 9 minutes into the film, when the pigeons are all dying, the people run from Trafalgar Square into a building with large windows at the front. Moments later, we see several birds striking and breaking the windows. If you watch carefully, you will see that at least two of the birds that hit the window are, in fact, fish. This was deliberately put in by filmmakers as an inside joke.
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U.S. Navy aircraft carriers are not equipped with sonar (the only one so equipped had it removed in the early 1980s). The Petty Officer on the bridge says "Combat relay says that our sub has something on the sonar", the aircraft carrier doesn't have the sonar it is being relayed via CIC from a sub.
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Revealing mistakes 

Some of the lines holding the USS Abraham Lincoln to the dock are visible on the side as the camera sweeps around the ship, disappearing as they pass in front of the water. Also, the aircraft are arranged for display as if the ship is in port, completely blocking the catapults and landing traps.
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After the shuttle Endeavour hits the river, Beck deploys the speed brake, but in the shot with the police cars approaching, the speed brake is retracted.
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We see a man quickly pull his hand into his car after it gets burnt. In the meantime, shots of other things getting fried are visible, followed shortly by the man looking terrified in the car, while outside, someone walks calmly past.
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When Virgil is falling through the water it is clearly traveling at high speed, yet the digital depth gauge is counting feet at about 1 per second (922, 923 etc) which is less than 1 mph!
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While Josh and Beck are welding the main power lines to the hull of the ship, Beck hands Josh the last wires and lays her hand right on the hull. Although the outer core is at 9000 degrees, the hull is extremely hot. Beck would have seriously burned her hand on the hot hull.
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While Josh and Beck are trapped with no power, in reality, the ship would have been pitch dark with no light. But there seems to be lights on the outsides of the panels.
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When Bob and Beck pull up to the base in the car for the first time, Virgil is already under construction before Josh starts talking about the mission.
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The ship crashes into the crystal and comes to a dead stop. Inside the ship, all the characters rock forward violently except Josh; when they stop, you can clearly see he realizes his mistake and mouths a curse word.
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Spoilers 

The goofs below may give away important plot points.

Audio/visual unsynchronised 

Shortly before the two remaining survivors get rescued, the sonar on the carrier is switched to speakers and we hear the sound of humpback whales. But the whales actually circling the remains of "Virgil" are killer whales (orcas).
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Character error 

Near the end of the movie where Rat's computer sends the "secret" information to the Internet, the message on the screen is "On It's Way".
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Character error 

In Josh's narrative, he says that the ship is divided into 6 sections. In the diagram on the screen, there are a total of seven sections. The last one ejected, which was not mentioned in the list, is the nuclear reactor compartment.
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Errors in geography 

When Rat sends information to news networks, when he reaches Al-Jazeera, the message says "Al-Jazeera, Riyadh, Saudi Arabia", but Al-Jazeera broadcasts in Doha, Qatar.
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Errors in geography 

At the end, computer graphics display a map of the world and show a document being sent to eight news organizations and the United Nations. As the locations are listed, the city, country, latitude and longitude are included. The first three (CNN, ABC, and CBS) display the correct cities (Atlanta and New York) but use the same latitude/longitude of 38 N / 97 W which is near Wichita, Kansas. All nine of the organizations listed show significantly inaccurate lat/long values except for the United Nations (which, for some reason, is in Belize City, Belize). In addition to this one of the news organizations he contacts is "Der Spiegel" from Germany. On screen it says "Der Spiegel - Berlin, Germany". Both the publisher and the editorial staff are located in Hamburg, Germany.
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Plot holes 

Braz says the master override switch to manually eject undamaged compartments is in a crawl space. Yet Braz goes into the impeller outlet, which is how the crew to got in. You cannot walk in a crawl space.
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