While filming courtroom scenes, the location was hit by the 6.7 Northridge, California, earthquake. Kevin Bacon was handcuffed to a large table, he took refuge underneath, while an enormous crystal chandelier swung overhead. The warehouse studio was later condemned.
The real life Henry Young was a bank robber who had taken and brutalized a hostage on at least one occasion and committed murder in 1933 - some 3 years before being incarcerated at Alcatraz. He had served time in State prisons in Montana and Washington before entering Federal prison for the first time in 1935 at the U.S. Penitentiary on McNeil Island, Washington (which is now a State prison).
The warden in the film, James Humson, is based on Warden James A. Johnston, who served as warden of Alcatraz from 1934 to 1948. Far from being a befuddled bureaucrat, Warden Johnston was very much in charge during his tenure on Alcatraz. Johnston had previously served as warden of both San Quentin and Folsom Prisons prior to his appointment to Alcatraz, but he did not (as depicted in the film) serve as warden for all three prisons simultaneously. (This would have been impossible, because Alcatraz was a federal prison, and San Quentin and Folsom are both state prisons.)
In real life, Henri Young's defense was handled by two prominent San Francisco attorneys, Sol A. Abrams and James Martin MacInnes. They offered the temporary insanity defense, saying that Young's brutal treatment on Alcatraz had led him to murder his fellow inmate, Rufus McCain. The jury bought the argument, and returned a verdict of Involuntary Manslaughter, largely because the Alcatraz officials who testified at Young's trial refused to provide any actual details of prisoner treatment at the prison to contradict Young's defense. (Alcatraz officials and guards lived under strict rules not to talk about prison procedures when off the island, for fear these details would make it into the newspapers and be used by criminals in breakout attempts.)
According to Stephen Tobolowsky, Oliver Stone was originally cast as Mr. Henkin but did not show up on the day of filming. Mark Rocco called Tobolowsky to take over the role just hours before shooting.
The trivia item below may give away important plot points.
The real Henry Young remained at Alcatraz until 1948, when he was transferred to the Medical Center for Federal Prisoners at Springfield, Missouri. When his Federal sentence expired in 1954, he was turned over to the Washington State Penitentiary at Walla Walla to begin a life sentence for an earlier murder conviction. In 1972, at the age of 61, Young was released from Washington State Penitentiary, but he jumped parole and, according to Washington State authorities, his whereabouts are unknown, therefore, Young might still be alive.