When Ram and Flynn are back in their cells Ram is doing tricks with his identity disk. The close-up of Ram's hands show he has no gloves on. When they cut to a wide shot Ram has gloves on.
In the opening light cycle battle just before Sark kills the other program, the light cycles instantly change places from Sark's blue cycle on the left and the yellow one on the right to blue right, yellow left and then instantly back again.
When Flynn is scanned into the computer, he is wearing Adidas trainers. In all scenes prior to that, he is wearing Nike trainers.
Yori's headgear changes to a male's helmet while on the Solar Sailer, and back to a female's covering when she is off the Sailer.
When the escapees first spot the water, Tron runs to it, then Flynn, then Ram. But when Flynn reaches it, Ram is already there.
In the opening arcade scene a customer starts to play the Grid Light Cycle game. The first shot of the monitor has the bikes moving correctly orthogonal. The next shot of the monitor they travel at a diagonal. This was never part of the original movie or game.
(at around 28 mins) When Lora shows her direct terminal in ENCOM building (laser target area) to Flynn, he turns the computer on by turning the wheel on the printer. Some may say that he tries to put the paper in, so he could print out the evidence of the theft of "Space paranoid" game, but the paper is already in and ready to print. This is maybe not a mistake, just ignorance...
In Flynn's Arcade, a couple of kids are "playing" pinball machines that aren't switched on (visible at the top left of the screen in the overhead shots).
When Alan leaves his cubicle to see Dillinger (after he finds the Tron program unavailable), the line between the built set and the matte painting of the cubicles moves distinctly (clearly visible on the DVD).
When Alan is leaving Dillinger's office, the lit elevator button does not turn off when the doors open.
Why would Flynn walk away from the Space Paranoid game just because he shot a Recognizer and got High Score. Then they made it appear the game ended as everyone congratulated him and just walked away. This would never happen in a real scenario. You would play till you loose or loose on purpose. If you just walked away someone would get on the game and continue and the crowd would stay.
The time differential between the computer world and the real world is very ambiguous, with "two hundred microcycles" apparently a very long time for a program to experience, but in the real world only the space of a few seconds. While this would make sense for computer processing speeds, in many cases the MCP converses with Dillenger as events are also happening inside the computer world at relatively the same speed. In reality, the amount of time that the real world sees in the film would actually be hundreds if not thousands of years experienced for the computer programs.
When the printer is printing out the data for "Space Paranoids", the sound is that of a dot matrix printer and the printer is a daisy wheel printer.
When Alan walks to Dillinger's office at the beginning, the sounds of the footsteps do not match Alan's steps.
When Flynn runs through the computer halls shortly before he gets scanned in the computer, you see a crew member sitting behind a Cray 1 supercomputer and several others reflected in the glass on the same Cray 1.
Around the 24-minute mark, in close-up shots of Dillinger behind his desk, what appears to be the top of a crew member's head is visible in the lower right corner of the screen.
During the opening arcade scene, the audience is shown that Sark is actually inside the light cycle game and that the player in the "real world" is actually playing against Sark. Yet, arcade machines would not be tied into the EMCON network (in 1982 remote linkups of this nature were only for high end machines) and would be stand-alone game consoles. Sark is clearly a program inside EMCON and therefore wouldn't be inside an arcade machine located at Flynn's.
In real life, a bit has two states: on and off. The bit that Flynn meets has three states. When at rest it is a different-looking character than when it says "yes" or "no." The resting state is a complex, many-faceted blockish character. The "yes" state looks like an octahedron. The "no" phase is a very spiky, star-like shape.
When Flynn is playing Space Paranoids, as the camera approaches the group, he is hammering the buttons and flailing the joystick. When the game is shown it's a calm tank drive and systematic button press to shoot.