Continuity mistake: During the fight at the End of the Line Bar, Gem walks and stand next to Castor. Later she move to the left and sits on a couch for the rest of the fight. However, at the very beginning, right after Quorra jumps and protect Sam, there's a brief cut where we can already see her sitting there, too early.
Continuity mistake: Castor is dancing while the fight is going on below in the End of Line club, along with Gem to his left. Moments later, Flynn lands in the club, and behind you can see that Castor is gone. The next time he is shown seconds later, he is standing back in his original position. (01:17:25)
Continuity mistake: At the start of the light cycle battle, a blonde haired program says "you've got no chance, user, their bikes are faster than ours" the shot breaks to a wide angle and in the same voice we hear "use the levels" but it's one of the other programs with dark hair left standing with Sam as the blonde haired one is riding away.
Continuity mistake: Immediately after the first round of Disc War, the revolving 'Jumbo Screen' above the arena changes from 16 combatants to 8 combatants (viewed from CLU's Throne Room). The next shot looking into CLU's Throne Room (with the revolving 'Jumbo Screen' reflection on the Throne Room window) the list of combatants incorrectly reverts back to 16 combatants. (00:32:00)