Actually, the only item that really bugged my logically were some of the environments (clouds, water?).
I guess I have no problem with either of these because the first movie established that the original Grid already had both. When the graphics show us going through the original Grid's sky there are clearly shapes meant to emulate clouds, the new Grid's clouds are just higher resolution (analgous to video game clouds from an Atari game versus a PS1 game).
Regarding water, there was a whole sequence in the original TRON that revolved around our heroes drinking "water" right out of their Identity Discs to recharge. Indeed, homage was paid to this when Quorra drinks at the dinner table and the drink lights up against her face.