As Madison Carter (Kelly Lynch), is trying to free Parker Barnes (Denzel Washington) from the virtual world at the end of the movie, Barnes' Neural Sens. meter clearly shows at 800 percent, and climbing. The next shot shows a close up of the meter and it is only showing 689 percent, and it climbs up to 800.
When Sid 6.7 is in the TV studio in front of the blue screen, an on-air shot shows just his head and shoulders superimposed on the skull backdrop, the next shot shows him standing in front of the blue screen with his arms crossed and his right hand holding a gun in a position that should have been clearly visible in the on-air shot, but wasn't.
When Sid steals the police cruiser and dumps Parker off he spins and does a 180, while taking off the light-bar on the cruiser is missing all but it's outer rotating lights but when the cruiser is approaching the tanker for a standoff with Parker all the lights are intact and functioning.
When Darryl first interacts with Sid on the computer, it's supposed to appear as though they are looking directly at each other. However, Darryl is standing off to the right (facing the monitor), and Sid is looking to the left.
Glass is mostly silicon dioxide (or silica), silicone is a synthetic polymer which contains silicon along with carbon, oxygen, hydrogen etc. So regenerating body parts with glass alone is just not possible.
Parker Barnes is arrested for allegedly shooting and killing SID's hostage at the train station, and later he is accused of killing the policemen who were taking him back to the station after SID murders them and "frees" Barnes (because he wants to see Barnes die a painful death when the satellite-linked chips explode in his brain). The problem is that both of Parker's alleged crimes are not plausible at all; if he shot the woman it would be obvious from the pattern of her wounds (since he was firing at SID from the front and SID fired at him, and shot and killed the hostage, from behind her) and he had his gun taken away and was handcuffed by the police before SID arrived for the murder/set-up.
After Sid's hand is blown off by a security guard's shotgun in scene at the fight arena: He jumps the fence to escape the ring after he spots Barnes, and you can clearly see the fact that a 'hand' is still present by the way the actor (or stunt double) uses that hand to help hop the fence.
The goof item below may give away important plot points.
During Barnes' flashback scene where his family is killed in the explosion Barnes sets it off by tripping the laser sensor. When Barnes is blown back by the force of the explosion the stunt wires are clearly visible on Barnes/stunt double.