My guess is that the $50 GC was applied to one ticket, and the remainder was treated as airline incidental fee charge and eligible for fee credit. The second ticket was seen as a whole ticket purchase and thus not eligible for fee reimbursement by T&Cs.

" Airline tickets, upgrades, mileage points purchases, mileage points transfer fees, gift cards, duty free purchases, and award tickets are not deemed to be incidental fees. "