U.S. Magistrate Judge Michael Wilner said Friday he was hesitant to grant bond to Oluwaseun Noibi based on the circumstances of the case.
Another hearing will be held at a later date regarding whether the man might be released on bond.
Authorities believe Noibi, 24, has been living in the Chicago area. On his Facebook page, he describes himself as an African missionary, and he brags about his air travels on his Facebook page.
Noibi was allegedly caught on Friday using an outdated boarding pass with a different name on it to get on a Virgin America flight from JFK Airport to LAX. The flight crew became suspicious of Noibi during the flight, and he was questioned on the ground in Los Angeles, but then he was released.
On Wednesday, he allegedly tried to do the same thing again. This time, it was on a Delta flight, but he was never able to get on a plane.
Authorities say they found a number of boarding passes in his possession.
Security experts say 10 years after the Sept. 11 attacks, the incident shows that the U.S. still has a long way to go in terms of airline security.
"We could have the best technology, you could have the best processes and plans, but again, it comes down to the human factor and human error," said Joseph Morris, a former TSA security director at JFK Airport.
Virgin America admitted there was a security breach in a statement, and said the airline is working with the FBI in their investigation. Virgin is also looking at their training program to make sure another incident like this one doesn't happen again.
"It appears staff may have missed an alert when the passenger presented a boarding pass from a prior flight," the airline said in a statement.
Noibi is facing federal charges for being a stowaway.