Minor Plot hole: When Quorra is restored by Kevin Flynn after being beaten by Clu's henchmen, she wakes up and mentions that Kevin's disk has been stolen....unfortunately this event happened after she collapsed and it is impossible for her to know that.
Minor Plot hole: In the final action scene, the heroic trio tries to beat Clu and his soldiers by outmaneuvering them with their light jet. The flying vehicles leave solid contrails that can destroy anything that touch them. In one specific sequence, Flynn's light jet goes into a complete vertical ascension path until the engine can't push it any higher; it then follows the same vertical path downwards. This would mean the destruction of the light jet since it would collide with the solid contrails it expelled going up a few seconds earlier and the contrails of the enemy light jet. But obviously, those contrails disappear so that he heroes can survive an otherwise suicidal maneuver.
Major Plot hole: The main antagonist, Clu, is blessed by lady luck when the random message he sent to the arcade made Kevin Flynn's son appear and re-open the portal between the Grid and the real World. Instead of using him as bait and hostage to lure out Kevin Flynn in order to get his identity disk (his main objective) he puts him in games in order to be killed. (Where he personally tries to do in the light-cycle battle).
Major Plot hole: When Quorra saves Sam Flynn from the games and escapes with him, it is explained that Clu and his henchmen cannot follow them outside of the Grid because their vehicles are not adapted to the rough terrain. This however does not stop Clu and his henchmen later on to reach the secret hideout with space ships. And the hideout was not THAT secret, it was the only place outside of the grid that was emitting light.
Unaddressed Issue: It is never explained what Clu's plan exactly is. He wants to conquer the physical World while never actually knowing what it looks like. His plan's vagueness is equally matched by the underwhelming weight of his offensive capabilities. He plans to take over the World with a few thousand soldiers with short-range weapons. Can he create more ? Will they be real physical entities or computer programs ? If they become real physical bodies, will they die when the thousand of them cannot hold into the small basement of the arcade? Did the writers care?