The old problem of confusing transit pax with transfer pax. The CAA figures will refer for example to pax from ISL transiting through MAN to JFK on a through flight.
flybe pax transferring from say Exeter to EY at MAN will be included in both the domestic pax figures and the scheduled international. i.e. will be counted 4 times for a return flight under terminal pax.
Hope this is right but it's how I understand it.