Factual error: Sam is driving through a tunnel and there are also other cars driving through it. However, there are two X signs displayed in the tunnel, which should indicate that the road has been closed off and that no-one should be driving through it. (00:06:00)
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)
Audio problem: The synthetic effect on Gem's voice is missing when she says "Relax, they're occupied" to Sam whilst escorting him through Zuse's club. (01:09:00)
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: 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: 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 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: 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: 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 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: 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.
Other mistake: When Sam Flynn first enters the arcade, he goes to a breaker box on the wall. When he opens it, the breakers are already in the "ON" position, closest to the center. He actually turns them to the "OFF" position.
Answer: Because Clu was given all the authority of the most important user, the creator, Flynn.
Phixius ★
But what did Clu do to Tron to make him serve him? Tron fought for the Users so it would make no sense for him to suddenly side with Clu who wanted to create the perfect system and help him in annihilating the ISO's.
When Clu and co. attacked Tron and Flynn, Flynn's disc must have been damaged, removing his personality in a way similar to amnesia. This allowed Clu, now master of the system, to gain control of Tron's skills. Later, when Prinzler saw Flynn, he remembered him and what he did, and regained his original purpose.
The answer was in the movie itself. During a conversion between Sam and his father it is mentioned that Clu had the ability to repurpose programs. This is the action that allowed him to "build" the perfect system. The isos were manifested without creation from anything and had genuine freedom that Clu couldn't repurpose. This is why he destroyed them because it threatened his strategy to create perfection. Answer: Clu repurposed Tron to serve him and do his bidding. That simple.