‘every little helps’ – huge corporations can not afford to get bogged down in looking at each individual case or they would need thousands of call center workers with alot more authority, and in that case it then is costing them more money.
Ive never seen the sense in economy travellers even having a membership card, as it is almost impossible to build it up unless you are travelling ALOT. Membership programs just are not designed for the economy traveller, as the great majority of economy travellers will have no brand loyalty, they want the cheapest most conveinent option.
I am being very general here, and i know there are exceptions to everything. but….
In regards to you not getting your miles on just one sector, well maybe your ticket was a multi class booking, for example V outbound S inbound, and one accrued and one didnt, quite common.