Instead of purchasing goodybag on your account you might have purchased an airtime balance that might be one the reason your balance got deducted as per normal rates.
Airtime balance and goodybag are two different top-ups.
> Goodybag is bundle of calls, text, data and free giffgaff services and it's valid for 1 calendar month.
> Airtime balance are used for making international and premium calls. As goodybag won't work for making any international and premium calls.
To get more helpful information on goodybags and airtime balance, you can check here: https://community.giffgaff.com/t5/Help-Support/What-is-the-difference/m-p/4713140/highlight/true#M16
To confirm this, you can Contact an gifgaff agents from here: https://giffgaff.com/support/ask
and check about your missing balance.