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.
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.