What went wrong

[whitehall]

The FBI already had a tip that at least one of the brothers was a potential terrorist. Indications are that he was interviewed and his name was never entered into a data base.
There were hundreds of Police in the area but apparently everyone was asleep on Thursday night when the car chase happened and the young brother got away.
The terrorist must have been watching the search and entered the boat after the Police had passed.
The all clear was sounded a bit prematurely and the owner of the boat could have been killed when he found the terrorist crouched inside.