Plot hole: The whole movie plot relies on a very unlikely assumption: that the ex-husband would not visit Kidman at her mental institution where he put her in, nor call for any news at all, for four whole years... Even though divorced, they still share a common child! And what about the parents / siblings / extended family/ friends of Kidman? Would they also never visit for four whole years? If any one of them had, then they would have known the (fake) ex-husband had taken her out and would have called the real husband to get news. Then Kidman would have been reported as kidnapped.
Revealing mistake: Throughout the film, the base station radio is not connected to an antenna. In many lengthy shots of the back of the radio we can see the power cord trailing out the back of the unit, but there is nothing plugged in to the antenna socket. This is especially annoying because base station radio problems are a key plot point.
Factual error: The solar panels (or mirrors) are facing away from the sun. The sun's position can be estimated from ground shadows and object highlights and the panels are facing in completely the wrong direction. (01:11:40)
Deliberate mistake: Despite taking place for at least three years (prior to the arrival of Thomas) in an isolated post-apocalyptic setting, the boys in the Glade have professional looking hairstyles, not the least of which are Minho and Gally, who both have short hairstyles that look evenly cut and professionally maintained.
Audio problem: Murph's dialogue doesn't sync with her mouth at the lines "you hate farming, Dad." (00:17:43)
Factual error: During the decompression the plastic water bottles crush. The opposite should happen, as a decrease in external pressure would cause the bottles to expand.
Factual error: During the final fight, Liam Neeson jumps down an aisle to pick up the pistol that is hurled from the floor upwards in the air and shoots the villain in the head. The problem here is with physics. The plane was in radical descent moments before. The pilot eventually brings up the nose. At that moment, the gun and Liam Neeson himself would have been pinned to the floor.
Factual error: Newgate makes a reference to Mickey Finn's name being the same as that of a Chicago bartender who used to drug his patrons with knockout drops. However, the film is set in 1899, but the real Mickey Finn wasn't caught until 1903.
Factual error: A scene shows a 1980's Ford Crown Victoria with New Jersey license plates. They start with QQ which means it's registered as a historic vehicle which means it has to be at least 25 years old. The film is set in 1999.
Continuity mistake: Roy is on his back at one point, seemingly knocked out. A shot later he's suddenly on his stomach before regaining consciousness.
Factual error: In a scene where Kat is flying to or from Northern California for college, in the background through the window on the plane one can see a commercial jet which has the winglets of a narrow-body Boeing, which were not introduced until 1998 on the Boeing 737 NextGen, rather than "wingtip fences" of an Airbus which were in use as early as 1985. Eve disappeared in 1988 when Kat was 17, so this would have been 1993 at the latest, when Kat would have been expected to have graduated from Berkeley. In the movie, it is suggested that this was just 2 years after her mother disappeared, so this would have been not later than 1990-91.
Revealing mistake: At the end the sides of the grave (which Jack just had dug by spade) are too perfect. Only an excavator could get such neat sides.
Revealing mistake: When the newscaster was filming Clinton giving a statement, the timer on the camera stayed at 0:00. The red "Rec" button, which supposedly was on, also looked fake. (00:10:35)
Other mistake: Elizabeth Banks' husband says it's 4 in the morning but there's daylight coming through the window.