This is the lack of a basic control :
They base their final passenger numbers on however many people have been scanned through the boarding gate.
The crew cant notice they are missing A passenger let alone a large number of passengers if they only rely on the boarding gate data.
However, the cabin crew should have noticed such a large number of missing passengers because they get told how many they're expecting.
I agree with PPs that experiened staff should notice as an estimation how many "blank spots" each side of the plane had but the security control around luggage unloading should not rely on guestimations.
Jet2 knew or should have known that there were multiple points where a passenger could relocate to/"hide" between the gate and the plane.
Failing to insert a control around that weakness is a security hole and management failing.