Drawing a blank. Don't remember anything directly pertinent from the movie (except that Tron shows up for about a minute at the climax).
Anything to do with the transfer process itself? Certainly seemed like a trap within a trap, and the light show with Tron's data being extracted seemed like a bit of an unfired Chekov's gun.
And possibly a rare moment of Tron actually depicting computer behavior in a sane and realistic fashion.
I had a brief moment of "Wait, how is Tron okay if they pulled his magic blinky-light self out and didn't put it back in?" before realizing that no, they're actually depicting a filecopy accurately for once. Of COURSE if Tron's data wasn't overwritten then it was still there; there's no such thing as actually moving data, only copying it or overwriting it.
Or possibly the glowy-light code stuff they extracted was just the virus and we're back to cartoon logic. But I like my interpretation better.