I believe Jet2 do not require a headcount if the aircraft is boarded via airbridge unless the captain requests one. Stair boarding however requires a headcount.
When families board flights. they normally pass you a stack of passports in one hand, and a stack of boarding cards in the other hand, with all the kids running around. It can be quite difficult for the gate agent to keep track as the parents allow there children to run where ever they want, including in and out of the gate. while the PSA organises the passport and boarding cards and keep track of the little ones running around. Plus the added pressure of minimal turn around times. Personally, I'm surprised this didn't happen sooner.
There is also the added possibility of parents being over protective of their children. I would thing quite a lot of people out there today are afraid to address children in fear of there parent screaming "child abuse" at them. Just look at how many people have complained about children being searched at security...That is also another factor in the puzzle here.
Besides, Who would ever think "that child over there is unaccompanied"?
The only changes I see happening, are head counts required on all flights. and to enforce the "passengers hold their own boarding cards" while boarding. It is requested in the boarding call that all passengers do this. However. Parents don't trust the little ones to hold their own ticket. Which is understandable. But It only makes PSA's jobs harder.
Or. Who's to say the kid didn't sneak behind one of the PSA's while they were checking other passengers Boarding cards? Nobody has eyes in the back of their heads.