Outside of the CP holder not on board (which I imagine is pretty rare), this seems happen too much for comfort if I was in charge.

Some significant process has gone wrong or is not followed - thru count off is or people are let on without being scanned correctly. Checking in then not showing up should have zero impact.

What else can it be? A stowaway on board? Someone got on the plane properly than ran off?

Seems real loosy goosy to me, math is math.