The first step is to reboot your handset, and then check the payment history on your MyGiffGaff page at https://giffgaff.com/orders/history
and make sure everything appears as you think it should.
If that shows the transaction(s) you were expecting, then check your GoodyBag's status by dialling *100*7# from your handset (the phone-based system often updates quicker than the website and the app). Under normal circumstances, GoodyBags are applied instantly, so there should be absolutely no delay between a confirmed payment and the GoodyBag working; you should also receive both a text and e-mail confirmation of the transaction (assuming you have notifications active).
If you find that the system is showing your payment, but not your GoodyBag, then contact an Agent at https://support2.giffgaff.com/app/ask/Top-up-balances-and-goodybags/goodybag-allowances-or-credit-balance-incorrect/form/
and they should come back to you within 24 hours, however, they're usually much quicker than that. You'll find any Agent replies at https://giffgaff.com/support/questions
(you should also get an e-mail when a message is received there).