the issue is - you have to remove the unwanted frequent flyer number before you add a new one (and that can usually only be done by an agent who knows what to do). flight segments can have more than one frequent flyer number attached. which one gets displayed is either the first entered or the last entered one (depending on the system) - even the number on your boarding pass might be the incorrect one for the mileage credit. with ITA airways you could use a trick to double dip for a long time to collect with ITA and another program on the same flight (ITA flight booked with ITA number and after checkin change of FF program to another one - > both programs received mileage and status credit).

moreover there are two separate internal fields for frequent flyer numbers - FQTV and FQTS - FQTV is for mileage earning and FQTS for status perks. Website editing of frequent flyer numbers might not update both fields in sync - so that could be another explanation for FF number chaos if not reset properly.