The CAA operator figures are based on data supplied by the UK AOC holder, so if the data is garbage, it can't be anything other than the garbage that has been supplied by Flybe to the CAA. It's a different data collection methodology to the monthly pax figures by route which are supplied by airports and are erratic, particularly when multi-leg flights are involved.
Emerald is operating on an Irish AOC and so doesn't supply data to the UK CAA. That will change if/when it gets its UK AOC, just as for Ryanair.