They don't count passengers during boarding - it's too chaotic for that. They are supposed to look at the boarding passes. If they scan them, the computer is supposed to tell them that the pass is no good. The system failed right there and then.
The head count was done after the takeoff because that's when you have a chance to count passengers - they aren't moving around at that time, but the crew can easily walk around since they know how many minutes remain until the actual takeoff.
Then, although Noibi was reported to the FBI and questioned after the plane landed, he was RELEASED.
And that is a shame. Obviously FBI doesn't think that Nigerians anonymously flying within the country under someone else's name and defrauding the carrier are not a threat. However John Smith, flying under his own name, will be held at gunpoint because one of millions of Johns Smiths did (or just as likely haven't done) something untoward a few decades ago.
The country is solidly in decay, and the law enforcement is not an exception. FBI just can't be bothered with petty matters like an unidentified Muslim flying under someone else's name, and they don't want to know how that Muslim got to own those expired boarding passes. It's much more fun to grope citizens who honestly paid for their tickets.
The FBI said Noibi stayed in L.A. for four days and then tried to pull the same stunt on a Delta flight to Atlanta, again, with no valid ID or boarding pass. But security officers caught him with 10 expired boarding passes in his possession and he was taken into custody. He was charged with being a stowaway, but not under any terror or security laws. He faces a federal court hearing Saturday.
I wonder: what is the point of having a manifest, if it is not checked against a head count BEFORE takeoff? It’s been awhile since I worked at the airlines, but I thought that was how it’s done.