Corrected entry: After Flynn, Tron and Ram escape on their light cycles they decide to dismount them. The stick that was presented to them in the game grid to create the light cycles disappears and breaks apart when they dismount their light cycles. They even show a look of surprise when the stick breaks up. Because of this they should not be able to recreate the light cycles, yet after they drink the "power" water they are once again riding light cycles.
Corrected entry: When Flynn hacks the keypad and opens the giant security door, look carefully on the back of the door for a pressure handle similar to those used on Fire Exit doors. This is ridiculous. No one could physically move a metal door of that size.
Corrected entry: During the main lightcycle sequence, there's the part where Ram and Tron kill the last blue bike by converging; this is not possible for them to do (the bikes don't even turn, just magically move closer). Also, there's no way for them to have gone through the crack in the wall at the same time (and they can't go in separately, because of the jet trails).