The PIA incident is an interesting combinations of failures:
- Misguided pax
- Failure by CC to have her removed at CDG
- Failure by Ground staff to removed her at CDG
- Failure by new CC to have her removed before departure
Consequently, there is probably part of the story missing.
Yes, the missing part is that the CDG arrival and subsequent departure is timetabled as a through flight from Milan/Malpensa (PK734 MXP-CDG-LHE).
I don't know whether the Italian-originating pax would have stayed on board the aircraft during the 1:20 stop at CDG, but if so that could well have accounted for the one extra pax being overlooked (though it doesn't excuse the absence of a headcount).