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," and when it says, "no."
The at rest state is a complex, many faceted block-ish character. The "yes" state looks like two 4 sided pyramids joined at their bases (octohedron). The "no" phase is a very spiky, star-like shape.
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 Sark has his power cycles slowed down by the MCP the first time (0h:33m), the shot from behind Sark has his arms flailing about, but the front shot of Sark shows his arms holding on to the panels.
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.
Towards the end of the film, one short sequence involving enemy craft is rendered entirely in traditional cel animation, using a bright "cartoon" style that is jarringly different from anything else in the movie.
(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 one scene on the light cycle grid, we hear one of Sark's forces (the ones piloting the blue cycles) say "I'm taking him into the maze!", but when we see the cycles turn and head into the maze, Flynn's cycle (in yellow) clearly has the advantage.
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).
The goof item below may give away important plot points.
Ram has just died and the next scene shows Tron running down a corridor. As this is occurring, there's a black speck to the right that's crawling around in a circle indicative of a bug on the transfer screen.