Why wasn't Link arrested after the events of "The Reward"? I assume, given how Pavel planned it, that he got the blame for framing Hopper as the Renegade, so why is he still free after that episode?
Link only reported Hopper and the lead worked out. There's no proof Link framed Hopper, and Tesler would just as soon pretend the debacle never happened.
Why didn't Flynn cure Dyson's wound back in Scars? That would have prevented Dyson's betrayal and the tons of drama that ensued.
Flynn probably thought that Dyson would get the repair work done himself. I also doubt fixing his face would have done that much to sway Dyson's opinion.
Well, now Flynn just acted like a Jerkass God and sealed his own downfall.
I have the feeling he didn't ask Flynn to heal him since he already turned to Clu's side.
Also, why didn't Tron do anything to convince Dyson that it wasn't the ISOs who caused the riot? He could have showed him the memory where he notices a provoker among the ISO crowd.
He saw no proof that the provoker wasn't an ISO. All he saw was a shadowy figure running away from behind the crowd.
In both movies, programs are given new Identity Disks. In the second movie, we even see that it loads memories onto the disk. Why didn't Tron and Beck just try to get one of those? Sure, they had reason to get Beck's original disk back, but getting a new one would have kept Beck from becoming a liability during the search.
Even if one were to assume getting a fresh disc were a simple matter (I doubt it, based on everything Sam went through), there remains the problem that Beck's disc had his entire time as the Renegade and his knowledge of Tron stored on it. The longer they wait, the more likely the thief is to sell it to the occupation.
Why are there musicians in the Grid, but no singers? It can't be that they aren't programmed to, since Paige was dabbling in music despite being a medic (and later gained military training). Is it just that no one has put two and two together that voices can make music?
Why do programs project light walls from their light cycles when they're fleeing from someone? It only makes them easier to track.
Light walls de-rezz vehicles that hit them along with the programs using the vehicles.
It does make sense when they are pursued by a program on a light cycle, but in Rendevous, for example, Beck and Paige were not.
We have seen numerous times that a memory file in a program's disc does not show a video from the program's perspective. This is not logical.
Programs can actually use third person camera mode.
In "Tagged", what possessed Mara to go into Tesler's ship with Beck without her visor on? Pavel definitely knows who she is and where she works, and could easily have recognised her if he'd gotten a better look at her. Come to think of it, why didn't Pavel recognise her? He clearly sees her, albeit briefly, when she saves Moog and Rasket along with Beck.
Who says he hasn't? The next time they meet ("Terminal") he has all the time in the world to have her executed (or so he thinks) since he takes over the garage. And he outright orders her execution at the end. But yes, his lack of reaction in "Tagged" is still a plot hole.
Why (and how) did Tron trap Cyrus in his mirror world instead of just derezzing him? This is something that's never been mentioned, referenced, or even hinted at being possible anywhere else in canon that I'm aware of.
Tron and Beck together barely managed to subdue Cyrus and he still escaped. Tron back then had no other security program with the training needed to aid him and had to do with Sealed Evil in a Can.