Goof (anachronisms): During the opening scene, as the two guards are walking up to Alcatraz, you can see the San Francisco/Oakland Bay Bridge lit up in the background. Lights weren't added to the suspension cables until 1986.
Goof (continuity error): When Cobb is making his bed in his cell, the folding table in front of the toilet is up. When the camera switches angles when he sits down, the table is folded.
Goof (factual errors): It is stated that Cobb uses a Winchester Model 70, though he is shown assembling a rifle from two pieces. There is no version of the Model 70 that breaks down into two pieces.
Goof (factual errors): Detective Madsen speaks with a gun store employee who admits to selling a rifle to a man without a name or address. In actuality the employee would likely have been arrested and the store investigated as it is illegal to sell a firearm to anyone without at the very least a name and address so that a background check can be performed.
Goof (continuity error): It is said that Cobb purchased the rifle with a prepaid credit card. In the security camera footage of him buying the rifle, it shows him counting out cash.
Goof (continuity error): While Ernest is on the hill shooting at people at the carnival he clearly targets the head of the two people on the ferris wheel. Later when Detective Madsen and Dr. Soto are reviewing the crime scene, one of the police officials mentions that all the kill shots targeted the heart.
Goof (factual errors): A large chunk of plot is based on Alcatraz having a commissary (i.e. a place to buy items not issued by the prison). However, rule 49 of the inmate regulations famously states: "49. SPECIAL PURCHASES: There is no commissary at Alcatraz. The institution supplies all your needs. You are not allowed to have anything sent to you from home, friends or relatives".
Goof (anachronisms): The aerial view of the bridge spanning the bay is the eastern span of the San Francisco Bay Bridge which will be replaced by a new span which is under construction and should be clearly visible in the contemporary scenes.
Goof (factual errors): Every time Guy pulls out his 1911 .45 pistol, there is a sound of the hammer being pulled back and/or the safety being taken off. However, Guy is consistently shown with the gun in his left hand, and the thumb safety switch on a 1911 is on the left side of the frame (side opposite of your left hand's thumb). It is possible he's left the safety off, and is thumbing back the hammer, but this would mean he's carrying it with a round in the chamber, and the hammer down, with no safety - the most dangerous possible way to carry a 1911 (known as "Condition 2"). A slight tap on the back of the hammer, while in this condition, would set a round off. As a trained guard who carried a 1911 often, he would have known better.
Goof (continuity error): After McKee takes out the train driver, he pulls the window shade down. When he talks to the passengers over the PA, the shade is up. After he releases the gas, he raises the shade.
Goof (factual errors): When the map of the bay is shown, the name of San Francisco is spelled as 'San Fransisco' for both the city and the airport.
Goof (factual errors): When the map of the bay is shown, South San Francisco is spelled as 'South San Fransico'.
Goof (factual errors): In a flashback sequence it shows what appears to be a Catholic Mass in the prison but the Warden is invited to "give the homily". The Catholic Mass does not permit lay people to give the homily.
Goof (revealing mistake): In the last scene Warden James picks up a gold ingot with one hand and marvels at it. A gold ingot of this size would weigh at least 40 lbs and wouldn't be that easy to pick up and hold.
Goof (revealing mistake): Clarence Montgomery's first victim on the golf course is clearly breathing.
Goof (anachronisms): The type of adhesive strips places on Clarances eye lids to keep them open while he receives shock treatment, were developed after 1963.
Goof (revealing mistake): When Hauser and Madsen enter the apartment we see Madsen start to pick the lock. Cut to the inside of the door as it opens... we clearly see the rimlock is pinned open.