Continuity mistake: Tron sends his memory disk to talk to Alan. After Tron communicates with his user Alan1, Alan sends him back the disk with new data on it to destroy the MCP. When Tron receives the disk it is like a Frisbee, solid on the top and hollow on the bottom. When he receives the disk the hollow part is on the bottom. He holds the disk in front of him and starts talking about "the key to the new order". The shot changes and the disk has been reversed, hollow side toward him and solid side away from him. He did not have time to rotate the disk. (01:08:10)
Continuity mistake: When Tron fights off Sark's men as they board the Skyship, watch for the soldier who falls off the side just after Flynn. It's obviously a still rather than an actor as only a pair of non-moving legs fly past the ship. It's an editorial mistake as had the character been "derezzing" (deresolution) he would have glowed yellow and faded which did not happen here.
Continuity mistake: In the initial Lightcycle scene, the bikes inexplicably change position: In the beginning, Sark's blue cycle is on the left, but after they turn towards the arena wall - just before the user worshipper crashes - Sark suddenly races on the right side; and there is no sign that he changed tracks in between shots. (00:01:20)
Continuity mistake: When Flynn, Tron, and Ram are in the lightcycles, most of the time the cycles are red, yellow, and orange. However, in one shot where the 3 of them have left the game grid and are speeding away from their pursuers, the cycles are shown as red, yellow, and green. [This has been corrected in the special edition re-release.].
Continuity mistake: From the Light Cycle grid, the hole in the wall made by one of the Blue bikes has a jagged side like the teeth of a saw blade on the left side, and a couple of squared projections on the right. The hole goes all the way through to a tunnel on the other side. When the trio escape, and exit out into the tunnel, the hole has the saw-tooth jagged side on the left instead of the right. It should be a mirror image of the Grid side of the hole.
Continuity mistake: When Alan is typing to get access to TRON, his hands are reflected in the screen. When he's done typing, his hands and then his arms move back to a relaxed position. When the camera cuts to his face you can see his shoulders move as his arms are pulled back from the computer to a relaxed position again.