(at around 7 mins) When Gandu 3 Echo is called out of the elevator for creating a disturbance, we can clearly see the label on his sleeve is "G3A", which would incorrectly signify that he is of the Alpha generation.
(at around 1h 40 mins) When the two Lincolns are driving to the news station, they are stopped at a light when wreckage falls directly in front of them. Somehow it is cleared for them to speed away and the wreckage is no longer visible.
When Lincoln Six Echo decides to go back the facility to save everyone else, he has a large cut on just his right cheek. When he is in the helicopter on the way there, it has moved to his left cheek, facing the camera. When he gets to the facility, it has moved back to his right cheek.
When Jordan Two Delta nails the bad guy's hand to the door, Lincoln Six Echo hits him twice in the head with a crowbar. In the next scene, the man is yelling in pain from having his hand nailed to the door. And later seen bandaging his hand, but no marks on his head from the crowbar.
(at around 1h 40 mins) When the two Lincolns are driving to KNBC the car stops over the stop line at a red light. In the next shot the car is only half way over this stop line. Even more, when the car accelerates, it starts far from stop line.
When Lincoln Six Echo and Jordan Two Delta are running from the facility you can see their white tracksuits getting dirty, then when they are outside their white tracksuits are clean with no spots. Then in the next scene they are dirty again.
(at around 46 mins) While Lincoln and Jordan were running through the conditioning room (where it was pouring water) they were both wet and dirty, yet when they ran into the next room, they were perfectly dry and clean.
When Lincoln Six Echo and Jordan Two Delta see the boat sitting on the dock, it is visible out the window. In the close-up shot of Lincoln Six Echo, you can see a limited area of the dock, but the boat is missing.
When the Laurent Team Members are chasing Lincoln Six Echo and Tom Lincoln and entering the warehouse, the right door of the car opens. Then in one turn, at one moment, it is closed, and right after is open again.
(at around 1h 22 mins) In the shot through the windscreen of the Black Wasp as it begins its descent over the freeway, a camera and three crew members are briefly visible in the bottom left corner of the frame.
(at around 1h 21 mins) The train wheels falling off the trailer fall and flip towards the pursuing police. In reality they would continue moving in the same direction as the semi and flip in the same direction.
At around the halfway point of the movie Albert Laurent is checking Lincoln Six Echo's (and Tom Lincoln's) details in the helicopter. Under 'vital stats' the Metric measurements are way off. Apparently they are 435cm tall and weigh 210kg.
(at around 1h 20 mins) Lincoln and Jordan hide on a truck carrying train wheels, even though previous scenes show that trains no longer use wheels. However, these rusty wheels could have been on their way to the scrapyard.
McCord explains to Lincoln Six-Echo and Jordan Two-Delta that by their naming, Lincoln (being an "Echo") would have been from the third generation, and Jordan (being a "Delta") would have been from the fourth. Following the actual military naming of the clones' generations in alphabetical order (Alpha, Bravo, Charlie, Delta, Echo, Foxtrot, Gulf, etc.) would have, in fact, placed Lincoln in the fifth generation, not the third. However, Lincoln had asked how old they were, not what generation. McCord was telling them their age. Lincoln was Echo generation and is 3 years old, Jordon was Delta generation and is 4 years old.
Clones (or twins) do not have the same fingerprints, neither they have the same retina. While twins do not share the same fingerprints or retinas, clones do. Clones by definition are a copy of the original, and therefore would have the same fingerprints and retinas.
In the conditioning room, clones are implanted with the desire to go to the Island using footage of a talking head. However, earlier in the film the clones are shown taking remedial English lessons. By the film's own logic, newborn clones would not understand any of the verbal conditioning.
When the Laurent Team Members are chasing Lincoln Six Echo and Tom Lincoln and entering the warehouse, there is a short scene during which front of the Cadillac is clearly visible with no extra camouflage, just genuine front side.
(at around 1h 18 mins) In several quick shots of the armored car smashing into the police car, the police car is clearly a mocked-up front half of a car with dummies in the front seats. Also, several cables and at least one Eyemo camera are visible next to, inside and under the gray SUV that the police car is pushed into.
When the security team are returning Jordan Two Delta to Merrick, the Pilot of the Helicopter is the same one who was killed earlier in the film when the giant R logo crashed into a previous helicopter, causing it to explode and plummet to the ground.
(at around 1h 23 mins) During the freeway chase, when the Black Wasp's gunner opens fire on the Mack truck, the arm of the gimbal suspending the Wasp over the freeway (to simulate flight) is reflected in his visor.
When the nail gun is used on the bad guy, you can see that the nail gun has an attachment fitting for compressed air. However there is no cord hooked up to the nail gun. Thus, no compressed air, no nails being fired.
The goof items below may give away important plot points.
Merrick explains one part of keeping the clones in line is by closely engineering all their entertainment to promote passive, non-violent, compliant behavior. Yet earlier, in the clone "nightclub", we're treated to the image of Lincoln 6 Echo and Jordan 2 Delta smacking the stuffing out of each other in a holographic arena. Even if they don't really punch each other, it's hard to see this as promoting "passive, non-violent, compliant behavior."
There are numerous inconsistencies between generation names and clone ages. McCord can determine Lincoln's and Jordan's real ages by their generation designation ... Lincoln is an "Echo" so he must be three, Jordan is a "Delta" so she must be four. But Starkweather, also a Delta, has only been there for six months while Gandu, another Echo, has been there for seven years. Seven Foxtrot, presumably two, is brand new while Lima One Alpha, created only as a breeder, has presumably been there for seven years.
(at around 2h 5 mins) When the clones are running out of the bunker door at the end of the movie, slightly behind and to the left of Jones Three Echo, Gandu Three Echo can be seen exiting also. This is impossible since Merrick previously injected him with poison which killed him.