Corrected entry: After Flynn Sr.'s identity disc is stolen off his back AND then shown in Clu's transport (he has not stolen it back yet), we get a scene lasting several minutes between Flynn Sr., his son, and Quorra, where Flynn Sr. is standing with his back to the camera and his disc - which is supposed to be gone - is still there. When Quorra's disc is off, it is missing, and we do not hear anything about Flynn Sr. being able to spawn a new disc.
Corrected entry: Flynn's arcade had been locked up since the disappearance of Flynn in 1989. When Sam was walking through the arcade, one of the arcade machine was Mortal Kombat, which didn't come out until 1992.
Correction: Flynn disappeared in 1989 but they never say that the arcade closed down immediately after his disappearence. In the first movie it's explained that he took on the responsibility of running the arcade after he was forced out of ENCOM. At the end of TRON he's back in control of ENCOM and obviously had someone else running the arcade.
Correction: That's not Flynn's disc: it's Quorra's. Transporting it that way leaves both his hands free.
Sereenie