When the protagonist has been captured by The Kernel and is asked "Who is your user?" Why did he not reply "Alan Two"?
He didn't use Flynn's gambit of acting like a program.
Fridge Brilliance: Per the comic, "Uncle Kevin" told little Jethro a very sanitized version of his adventures. If Jet recalled any of it at the time, he probably figured admitting he was a User would help!
Wait, shouldn't that have been 'Alan 01', not 'Alan 2'?
Ma3a repeatedly refers to Jet as "Alan 2" Mostly because she thinks that Jet is the next version of his father, Alan. It could be that the system admin played a joke on Jet by making his username "Alan 2".
Kidnapping an executive from a Mega Corp. headquarters in broad daylight is anything but a subtle tactic. Ditto with all the breadcrumbs left behind pointing to Thorne and the fact he won't be coming back from cyberspace. How are Jet and Alan going to explain any of this to the police?
If damaging an uncorrupted User to non-functionality kicks them back to the analog world, as we saw with Flynn's Heroic Sacrifice in the first movie and the defeated Datawraiths, why does Jet as well as Ma3a and Alan die if he runs out of hit points?
The death could be that he does get kicked out, and seeing how the HQ is currently infested with fCon goons, they'd probably detain, possibly kill, him on the spot, which means the adventure is over. We just don't see that part. It would be even worse for the parts where the correction algorythms aren't installed.