Solved! Go to Solution.
Hey @Snicrich1129! Welcome to the Spotify Community. ^^
It seems you've subscribed to Spotify Premium through iTunes. Apple gets 30% of every transaction, that's why you are charged 12.99$ instead of 4.99$.You will need to cancel your iTunes subscription. This can be done by following the steps mentioned here. Then you have to resubscribe by going to the upgrade page.
After you've done that you can sign into the Student Discount again. And your discount will be applied on your next payment day.
Let us know if that helps, thanks! ^^