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: 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)
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.
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