Missing miles or not?

I booked flights for my son to join us mid way through our recent California trip. He flew out in Economy (X) to SFO and I paid for an Economy return upgraded to UC with his FC miles for the return trip from LAX on Monday. A spoilt boy and we had to be content with PE.
We have been unable right from the beginning to link his FC no. to the booking, but we were subsequently able to claim the missing miles for the outbound flight but after trying today the system would not allow me to claim his miles for the Economy portion of the inbound leg. Is this correct or should he be able to claim the miles for Economy ticket paid for?
We have been unable right from the beginning to link his FC no. to the booking, but we were subsequently able to claim the missing miles for the outbound flight but after trying today the system would not allow me to claim his miles for the Economy portion of the inbound leg. Is this correct or should he be able to claim the miles for Economy ticket paid for?