Here's what I think happened based on the reports at www.bbc.co.uk/news/uk-18980403.
He's an eleven year old and it's the start of the school holidays so MAN
Terminal 1 is packed out with families and groups. Kids often aren't trusted to keep hold of their own boarding passes and passport, which is entirely sensible. The lad mingles with a family or different families from airside to the plane and they think he's just ahead of/behind his own family, or something like that.
Manchester Airport no longer has dedicated staff checking boarding passes at the entrance to security, it's done by busy screeners when passengers are putting their belongings on the belt. These screeners aren't necessarily in a position to thoroughly check each child in a large group (they might not be able to see them even). Note; in Europe (unlike what the TSA do in the US), security checkpoints don't check ID, that's not part of their job.
Boarding the plane, mum/dad hands over boarding passes and passports to the handling agents and later boarding pass stubs to the cabin crew, this lad meanwhile mingling in with this family who perhaps aren't paying as much attention to him as they should.
Jet2's policy was that no headcount was needed, if the aircraft had been boarded via an airbridge directly from the terminal. All UK and Ireland based airlines the cabin crew have to check boarding passes, but headcounts are not compulsory. However, many countries don't have that requirement either.
Jet2's policy was not slack at all, since British Airways currently does not routinely perform headcounts either in these circumstances. Not that the media would tell you that. easyJet and Ryanair have compulsory headcounts on all flights (then again, the latter avoids airbridges wherever possible) and this incident may result in this procedure becoming mandatory on all airlines.
[Edited 2012-07-26 06:41:38]
"Freddie Laker may be at peace with his Maker, but he is persona non grata with IATA."- HRH Duke of Edinburgh