Yes thats very odd especially if its all just the way you described. For one thing I thought it wasnt possible and a national security risk for a plane to depart without the pax count matching the roster. If it says you flew but didnt actually then that means some boarding agents either cant count or didnt care. Ive been on many delays where pax count didnt match the manifests and we didnt move. One case 45 minutes delay looking for a missing pax and nobody could figure out who. Turned out to be a toddler where the parents actually bought a ticket but were holding the baby in their lap.

No worries by the fall of 2015 AS plans to add a feature to my wallet to keep track of credits