In Shangri-La, Edward jacks the action of his handgun three separate times without ever firing it. Loading a round into the chamber once would have been the most needed.
When Flynn falls through the bridge, and the camera pans out, you can see the same pieces of the bridge fall more than once (look at the farthest right piece fall - it falls about 3 times).
When Flynn climbs out of the river his bag is filled with water. The book was last seen in the bag, yet the book is undamaged by the water.
When coming down the stairs, holding the clue book, Flynn put the book in his backpack. After Judson taps him on his head, Flynn is seen holding the book in his hand.
As Flynn is talking to Charlene and Judson just before leaving the library, the book containing the language of the birds is alternately in his hand and in his back pack between shots.
When Nicole and Flynn jump out of the plane, you can see them rushing past the wheels of the plane. The landing gear is only down for take-off or landing, and they had not yet come close enough to the airport for that to have happened.
Airplane doors are conical in shape with the bigger frame on the inside. Thus the door will be sealed against the side of the fuselage by the pressure inside the plane. To open it you must first pull it inwards and then out which can only be done when the air pressures are equal on both sides of the door. You cannot blast it out of the frame the way Nicole does just before she and Flynn leaves the airplane.
When Nicole pushes Flynn out of the plane, he flies by the windows as people are asleep and reading. As soon as the door came off the cabin would have de-pressurized and breathing masks would have dropped. (The people inside the plane were not on another deck, which may have been separately pressurized.)
When given his initial tour of the library, he encounters the sword that Arthur supposedly pulled from the stone. This sword was unnamed in the Arthurian Legends; however, in the film, they called it Excalibur. Excalibur was the name of the sword that Arthur later received from the Lady of the Lake. Furthermore, historians generally consider the swords separate. This is a common misconception.
In the "scale model" of the Great Pyramid at the beginning of the movie, the walls are covered with hieroglyphics. There are no carvings on the walls in the Great Pyramid.
When Flynn and Nicole reach the temple in the jungle, Flynn refers to an astronomical phenomenon that "...circles the galaxy every 26,500 years...". The duration of a galactic year (the time it takes for the solar system and the stars in our vicinity to circle the galactic center once) is approximately 225-250 *million* years. However, he is actually not talking about the galactic year but specifically about Earth's axial precession, the movement of its rotational axis whereby it slowly traces out a cone. During this period, the positions of stars and therefore the constellations will slowly change in both equatorial coordinates and ecliptic longitude, and the 26,500 year time frame is correct.
When Flynn & Nicole step out onto the "invisible" floor in the Mayan death chamber, Flynn says the Mayans were the first to make use of mirrors. But there are several shots of the top and walls of the chamber and they bear no resemblance to the seeming abyss in the floor.
When Flynn wakes up in bed and realizes Nicole has left him, he gets up to look for her and the spear. He doesn't have to hold the bed sheet to cover his private parts, because it is obviously held in place with pins.
When Wilde hits Carsen against the wall of the replica pyramid, the stone wall flexes like it is made of plywood, drywall, or fiberboard. Approximate time 1:22:20.
Nicole Noone had just pulled Flynn up after falling off the ledge in a perpetual blizzard. Their (some how) ice-free goggles reflect multiple light sources on the Sound Stage - when at most there should be one, The Blotted out Sun.
During some scenes with Excailbur, you can clearly see a laser etched printed stamp stating "Made in (country not readable)".
When Nicole crashes the cafe, she is riding a BMW F 650 motorcycle which has a single cylinder engine but the sound heard is that of an in-line four-cylinder.
When they are on their way to Shangri-la in the mountains the set lights are reflected in their glasses more than once.
While camping out in the Amazon basin, Flynn points out several constellations including Cassiopeia. Cassiopeia is too far north to be visible in most of the Amazon and, even if they had been far enough north, would be too close to the horizon to see in the jungle.
When stuck in the Mayan "death chamber", Flynn says that the Mayan pyramid that they are in is an exact replica of Teotihuacan. There are multiple pyramids at Teotihuacan and that site is Aztec, not Mayan. The architecture is quite different.
At the end, when Nicole tells Flynn of the Deadly Scorpion
League, he wonders about the "insect names" for the bad-guy groups. Scorpions are arachnids, not insects. The first bad guys were the Serpent Brotherhood, also not insects.
When Flynn recites the line from A Midsummer Night's Dream he says "that WE have but slumbered here." but the actual line is "that YOU have but slumbered here." Puck is talking to the audience at this time and the word 'we' makes no sense.