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: Quorra's suit has a light stripe running down its right leg. When she's captured by Tron, the light stripe is now on the left leg. This is most likely a flipped shot as her fringe/bangs are also slanting the wrong way. (01:33:50)
Continuity mistake: At the end when Flynn is asking Sam to go, Quorra has Flynn's disc on her back. In the next shot she says "Sam, it's what he wants" and the disc is no longer on her back. And then in the next shot it's on her back again before she gives it to him.
Continuity mistake: At the end when Quorra and Kevin Flynn enter portal four, for some while Quorra is without the disk, and in the next shot Quorra is with the disk. (01:52:55)
Continuity mistake: Throughout the movie Quorra is seen wearing high heel wedge boots. During the fight scene at the club she is shown wearing a different flat soled boot. Immediately after the fight ends she is seen in the high heel wedge boots again. (01:17:20)
Continuity mistake: At the end when Quorra swings to the other side of Clu on the portal bridge she lands about a foot or two in front of Sam. But in the next shot when she stands up, she's right in front of Clu a good distance away from Sam.
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: Just as Flynn realizes Tron is alive, after he has captured Quorra, Flynn and Sam change from ducking their heads behind the wall to having their heads poking out.
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)
Answer: Going by Clu's behavior and personality in the film, Clu's idea of a perfect system was likely a system where every component worked as intended and as expected. One where every action by programs could be consistently predicted. The Isometric Algorithms very existence went against everything that he believed was "perfect", in that by their nature their actions could not be predicted. Users also seem to exist in contrast to Clu's beliefs as their human emotions cause them to act irrationally and erratically.