When Sam deactivates the screen saver on the computer hidden in the arcade, we see one window with, among other things, an indication that the machine he's working on is a sun4m. The first sun4ms weren't announced until about 1992, well after the time that Kevin Flynn disappeared.
The opening scene of the movie takes place in 1989. Kevin gives young Sam two action figures, and the figures have white LEDs in them. White LEDs were not invented until 1995, and due to their very high cost per unit did not see wide mainstream use until nearly a decade later.
The synthetic effect on Gem's voice is missing for two of her lines while she escorts Sam through the End of Line club. First when she says "Relax, they're occupied" and then shortly after again when she says "you want to speak to Zuse you're going to have to go through him".
During the disk wars, after Sam has defeated his first opponent, a banner above the arena can be seen changing to Sam's next opponent (unknown 3 vs Cray 7). In the very next shot, a reflection of the banner can be seen on the front glass of CLU's flying ship pairing Sam with his previous opponent (unknown 3 vs Pike 11).
During the opening sequence, the camera flies from the downtown area of the city, across the bay, to Flynn's house, and into Sam Flynn's bedroom. Thus, his bedroom window should face the skyline of the city. However, when he looks out of his window, there are no buildings visible.
During the fight in the End of line club. Gem is directly on the right of Castor. But after Quorra arrives, Gem is no longer directly next to Castor. When Castor pronounces "Behold! the son of our maker!" Gem appears on the right of Castor, but a few feet behind him. Then makes a motion as if to play his cane like an air guitar, Gem is now taking a seat right of Castor instead of standing. When Castor fires his cane, Gem reappears on the right of Castor.
The Ducati is the Sport Classic 1000 Biposto. It's often confused with the Monoposto version due to the removable passenger seat cover. This cover is in place through most of the movie, including when Sam arrives at Flynn's Arcade, but is removed when he and Quorra leave.
During the lightcycle battle each team begins with 5 lightcycles. Clu's team clearly defeats 4 opponents while Sam's team is only seen defeating 3 opponents. After the 4th opponent is defeated on Sam's team you see a wide angle view of the grid and only Sam and Clu remain. What happened to the 4th rider of Clu's team?
During the chase from the Encom Building and the two police cars pull out from the side streets on his left and right to stop him and pull up close together. As he looks behind him then again forward we again seeing the same two police cars pulling out from the left and right again.
At the beginning, Sam turns on two circuit breakers upon entering the Arcade, and everything turns on - lights and game consoles. At the end, when Sam turns off those same two circuit breakers, all lights and consoles stay on, as well as the marquee sign (Flynn's).
During the motorcycle chase, the motorcycle officer uses radar on Sam speeding through the tunnel. The officer's radar indicates 86 mph for lock speed and 103 mph for patrol speed. Patrol speed would be the speed of the officer if he were moving but since he was stationary, his patrol speed would be zero mph.
At the beginning of the film, which takes place in 1989, Flynn is talking to his young son Sam. Flynn did not have a son in the original 1982 film and so Sam should not be more than 6 or 7 years old during this scene, however he is clearly much older (played by Owen Best who was 12/13 when he filmed his scenes).
Ducati Sportclassic Sport 1000 headlight cannot be turned off. Sam turned it off when he was being chased by the police motorcycle, which is not possible if the first sentence is true but Sam had to do some work on the bike after it had sat there for 20 years, so it is not inconceivable that he had made that modification while he was restoring the bike to running condition.
When Sam Flynn is first brought to Clu, his identity disk on his back is not illuminated. The inner ring on both sides is always supposed to be lit, but several times in side views, various characters ID disks aren't lit.
When Kevin, Sam and Quorra board the Light Jet on the flight deck, and Quorra is making the jet lift off to escape, Quorra holds her hands in front of her as if using flight controls, but her hands can be seen open and empty and there are no controls or cockpit panel anywhere. In the next cockpit scenes, her hands are in the same position but now she is grabbing a joystick with the right hand and a thrust lever with the left.
When Sam bends down to pick up the quarter after it falls out of the coin return slot of the TRON video game, we see the side view of the cabinet for the "Discs of TRON" video game, which was the sequel for the original TRON video game. Beneath the logo for Discs of TRON, the Bally/Midway logo is seen, instead of the ENCOM logo, which was the in-movie distributor of the TRON video game.
When Edward Dillinger Jr. logs into the console during the board meeting, if you look very carefully during the cut-scene from his typing to the console screen you will see "Ubuntu" as the actual console root.
When the security guard is approaching Sam in the server room of ENCOM, he takes out a TASER X26, appears to release the safety and it makes a sound like a camera flash charging. The TASER X26 makes no sound when the safety is released.
When Kevin, Sam, and Quorra are traveling on the train to the portal, one of the trapped programs is seen moving. As the lights in the train go on, all of the programs are shown standing still with their eyes closed. The point is to show that the programs are "turned off" as they await their fate, but the female program closest to Sam is seen wobbling and swaying in two different cuts.
When CLU holds the speech in front of his army, there is a close up of one of his soldiers' helmets. CLU is seen mirrored right in the centre of the visor. In the next shot we see CLU standing on his podium yet not a single soldier is actually standing in front of him. The reflections on all visors should thus, with all soldiers looking straight ahead, either be on the left or the right sides of the visors, but never centered.