I think it is clearly obvious we have not had the full story so lets speculate.
The box went through the X Ray in the luggage area, something unexplained or untoward was seen on the X Ray. The passenger was asked at the gate to identify what was in the box he either made a statement that caused concern or was unable to identify what was in the box. He then had to go elsewhere whilst the contents where inspected and as a consequence this caused him to miss the flight. Therefore he was then offered a seat on the next available flight which happened to be nine hours later.