They were found on two beaches. A US border patrol spokesman said the case enhanced the realism of the exercise.
The two-day Operation Vigilant Sentry, which ended on Thursday, involved 325 agents and 85 law enforcement agencies.
Most Cubans who reach US shores are allowed to stay - those intercepted at sea are usually returned to Cuba.
Over two days, hundreds of law enforcement agents enacted a scenario which imagined thousands of Cubans fleeing violence in the event of the death of President Fidel Castro.
But the operation took on a renewed urgency when he temporarily handed over power to his brother, Raul.
President Castro recently spoke in a live broadcast with his Venezuelan counterpart Hugo Chavez, but has not been seen in public since last year.
Coast Guard Rear Adm David Kunkel said: "It's a mass migration plan in general. It doesn't have to be from Cuba.
"However we do recognise that Cuba is certainly an area where we must be prepared."