Continuity mistake: At the beginning when Indy is talking to Spalko, his hands keep alternating from being in his pockets to just resting at his sides between shots.
Other mistake: In the slaughterhouse scene, after Harrigan has injured the Predator with his shotgun and Keyes reappears, the Predator throws its disc, and severs Keyes in half at the waist. We see his legs flop to the ground, and blood pour from above, but his upper half (torso, backpack and weaponry) mysteriously remain hovering out of sight. (01:21:50)
Factual error: Towards the end of the film, Solomon is trapped in a small Plexiglas box and fires his gun into the bulletproof sides numerous times, but the bullets don't ricochet or get embedded in the glass.
Continuity mistake: In the latter half of the movie, Picard looks at a picture of himself from his days as a Starfleet Academy cadet while Beverly looks on too. This picture is actually the actor Tom Hardy (Shinzon, Picard's clone) and he appears with a completely bald/shaved head. Showing Picard bald as a cadet completely contradicts the TNG series. In the TNG episode 'Tapestry', a flashback set in 2327 (the year Picard graduated from the Academy), Picard is shown with a full head of hair. Also, in the TNG episode 'Violations', a flashback set in 2354 shows Picard with a partial head of hair when he takes Beverly to see her dead husband Jack's body. (00:46:25)
Visible crew/equipment: When C-3PO is on the conveyor belt, if you look in the reflection in his head you can see the camera crew.
Continuity mistake: When Layla is hooked up to the lie detector that tracks the movement of her eye, she is looking around the room and blinking repeatedly, but the eye on the screen (which is supposed to be hers) never moves or blinks, even though the camera is still on her.
Revealing mistake: While Poe leads the aerial assault on the oscillator, in the closeups of Poe and other X-wing fighter pilots, note the cockpit windows at the pilots' left and right have identical marks and scratches in their individual X-wings. It's particularly noticeable when one closeup follows another.
Factual error: Fitch, who professes qualifications in biology, genetics and biochemistry, says that they made Sil female because she's a natural predator and so she'd be more docile. He should retake his finals. In every single species of predator on earth - every single one - the females are the hunters, aggressors and killers. The males may be socially dominant but they are the 'docile' ones. There are no exceptions - and no human DNA was used to create Sil - they used synthetic DNA based on the instructions transmitted to them.
Factual error: The cavemen Harrier pilots are shown using the hover mode frequently. Harriers, even with drop tanks as depicted in the film, can hover for at most 5-10 minutes, as the thrust required to keep the aircraft in the air without any lift consumes massive amounts of fuel and overheats the engine, and real-life Harrier pilots are instructed never to hover for long periods of time, unless absolutely necessary. The amount of time the cavemen spent hovering (hiding out of sight in a parking garage, sneaking up on the Psychlo gunships, etc.) would have easily caused their fuel to run dry.
Character mistake: When Charlie is calling out the brick count to Napster from the subway, he describes it as being "13 across, 4 high, 4 deep". The bricks appear to be 2 deep in the safe (13x4x2), so he could just be lumping two shelves together, which works (13x4x4 = 13x4x2x2). The problem is that when the camera pans down there are 3 shelves in the safe. This means that there are more than the 208 bricks that Napster announces. (01:33:40)
Plot hole: The fact that a five minute timer starts after the three Cerberus codes are entered defeats the purpose of the program. If they program was made to destroy their own nuke warheads in case of a misfire you would expect them to be destroyed as soon as all three codes are in.
Other mistake: At the carnival, you can see an African-American man staring at the camera for a while. I am unsure if he is a crew-member watching over the scene, or if he is just an extra trying to get onscreen.
Factual error: A force of Russian Tu-22 Backfire bombers attacks the aircraft carrier USS John C. Stennis (CVN-74) by sneaking in under the ship's radar. This is all well and good except that carriers usually don't use their own radar, they have Airborne Early Warning aircraft (E-2 Hawkeye's) that can see much further and not give away the carrier's position (let alone the F-14s which would be patrolling too) not to mention the fleet of destroyers other ships guarding the carrier. The whole point is, the US Navy practiced and planned for such a "carrier versus Backfire" battle for years. I guess in the interest of furthering the plot Hollywood has to ignore the immense measures the USN takes to protect those multi-billion dollar assets, not to mention the 5000+ sailors that man them.
Factual error: As Ben is clinging to the staircase while it is falling apart, there is a close-up of a nail being pulled out of the wood. This nail is round-headed, rather than square as it would have been over 200 years ago. It's also shiny instead of rusty, which indicates that it's galvanized. Galvanization as an industrial, metal-preservation process was not patented until 1837, and was not used in building materials until well into the late-1800s. Since the film states the staircase was made by "the Founding Fathers, " and there was no galvanization of iron nails in any industrialized nation in 1780s-1830's, this is a huge anachronism.