* 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.
*** Wait, shouldn't that have been 'Alan 01', not 'Alan 2'?
*** Ma3a repeatedly refers to Jet as "Alan2" 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 "Alan2".
* A wee bit of FridgeHorror when playing through again. If Programs are, in a way, the "children" of their Users-Creators, then um...[[BrotherSisterIncest about Mercury and Jet flirting with one another...]]
** Programs usually look like the person that created them (The Grid from ''Film/TronLegacy'' was special). Either someone else created Mercury, or Alan has some rather strange secrets...
* Another one that could veer horribly into NightmareFuel or RonTheDeathEater. It was implied in-game that Ma3a is a cross of VirtualGhost and BrainUploading, her programming based primarily on the deceased Dr. Baines-Bradley. Was that accidental, or did Alan do that ''deliberately?''