The number on the back door of the stolen armored car reads "481516", which are the 5 first numbers of the Lost sequence. The missing numbers are 23 and 42. Jorge Garcia who plays Dr. Diego Soto was a series regular on Lost.
Goof: When Clarence and Megan Palmer are riding the golf cart in the beginning of the episode you can see cart tracks on the ground from doing the scene previously.
Small Goof: During the escape from the bank, Cal says "that Mustang has been following us for a while". If he was imprisoned since the fifties, and disappeared in 1963, how would he know what kind of car it was? The first Mustang didn't debut until 1964.
Nitpick: On the rooftop of the last shooting when you see Cobb looking through his scope. You can see a microphone under him.
The rifle Ernest Cobb uses is identified as a Winchester-70 with a suppressor-ready (threaded) barrel. According to the website winchester.com, there are two Winchester-70's listed as suppressor-ready (The Varmint Coyote, in black and stainless barrel style), but do not resemble the rifle Cobb uses (lacking the thumbhole, unique camo design of the stock and under-the-barrel vent holes). Unless the rifle was custom made and left specifically for him, it's unlikely he had the time to modify and test-aim/fire a different model.
While examining Cobb's shooting nest for the amusement park, Detective Madsen finds a shell casing, but picks it up in her bare hand, and then hands it over to Dr. Soto, contaminating what may be vaulable evidence. Madsen is SFPD detective-grade and should know better!
The door code to enter New Alcatraz is 6323.
Even though the show is set in San Francisco, and some of the pilot was filmed in the city and on Alcatraz itself, the producers of the show opted to film the rest in Vancouver, mainly because of the much more attractive production rebates than California and the city of San Francisco could offer, much to the chagrin of the San Francisco film industry.
The case file Hauser shows the gym employee attacked by Sylvane shows his middle initial as "F". On his death certificate, his middle name is Haughton. Also, the case file lists his date of birth as January 25th 1905 (which would have made him 58 in 1963!) while his death certificate says it's (a more believable) June, 1923. Also, the case file lists misconduct reports from McNeil Island dated 1910-1912, which (by the files DOB) would imply he's been incarcerated since he was 5 years old!
Lucy Banerjee (showing Detective Madsen and Diego Soto surveillance footage of Sylvane): Meet Jack Sylvane: 85 years young.
According to his death certificate, Jack Sylvane's date of birth was, June 18, 1923, which would make him closer to 89 years old as of the episode's airdate. It is also made clear this episode is set in the "present day", not 2008.