@Havanananana
I'm ex flight crew and have seen a bit of this, so I'm a bit wary of thinking one size fits all when it comes to how this works (for example things like headcounts are not universal, manifests are not all the same) hence my reluctance to jump in and blame the crew.
38 missing passengers would mean that the aircraft would be underweight by about 3,200kg so the pilots should have noticed this
Not when on the ground (unless things have changed and the aircraft onboard systems can display measured gross weight).
I can only really speak for one system but as an example usually for the sake of getting performance calculations done early the pilots would possibly have been presented with weights based on booked load/number checked in, and in this case that would include the missing passengers,.since they're not yet missing....hence no sign of an underload in those provisional figures to alert the pilots.
Later on, pre-take-off they'd.probably be given a set of final figures by hand/radio/datalink based on the number of passengers through the gate...now if the missing passengers hadn't gone through the gate then the underload would have shown up on the final paperwork...
Problem here is since they had gone through the gate their weight was on the final loadsheet, so on the pilots's paperwork so no obvious underload.
(I'll emphasise the above system is how a lot of airlines work but might not be how Jet2 do it)
IMIO the only time any underload/miss load might have been obvious to the pilots was if the take-off was unusually swift/sporty....or if the trim was significantly out as a result of the missing passengers.
I'd suggest the route cause for this probably lies with the airport system and the ground side of the operation