If the 63s are all appearing on Alcatraz Island, why doesn't the main cast just set up a few cameras to monitor the outgoing ferry? A few people in the loop watching screens all day could probably stop many incoming 63s cold. They could simply audit the ferry incoming/outgoing count, too. No need for cameras, just a clicker.
We only know of three confirmed re-appearance locations but two of them were on the island and one was far away on the mainland. They seem to appear at a place that had importance for them before they disappeared. Still after Sylvane they should be paying careful attention to the tourist traffic to the island. Guy Hastings seemed to have slipped by them without much problem.
The first season finale implies that the 63s returns were/are across the country
How are the 63s able to get around San Francisco after 49 years? They lived on an isolated island and didn't get around the city, locations change, people move, there are currently no phone booths, phone books. Did they learn how to use GPS technology or the Internet while they were in limbo?
Because the force that made them jump forward in time in the first place is currently unknown, it's possible that whoever or whatever did it gave them the knowledge to adapt to the modern world.
Streets haven't changed all that much in the city core. They even still run some of the cable cars. SF was well established in the 1960s, and like most old cities, many things stay the same. All they need is a map. It's a reach to say you need a GPS to get around a city. People have traveled to worldwide cities for decades without need for 3-meter positional accuracy. And a most-wanted criminal is going to need to get used to getting around strange cities a lot.
The more important question is how they can function in modern society without sticking out. Ernest Cobb and Kit Nelson probably kept low after they re-appeared but Cal Sweeney was very active and is able to fit right in. On the other hand, most of the 63's who return seem to be back to accomplish some task in particular. Jack Sylvavne was looking for that key, Guy Hastings was looking for Tommy Madsen, etc. It could be that Cal Sweeney had been returned some time back, accomplished his programmed task, and been learning to fit in ever since.
His programmed task was the key at the last bank. It seems more likely that they try to fit in and then go after their task.
Fridge Horror: In the final episode, Rebecca flatlines on the operating table. With the show cancelled, she can only be canonically considered dead.