Why are you worried about this? Have you been doing this a lot? Has one of your friends been arrested for doing this?
If it was a one-off event, you in fact told the store clerk the entire truth, he gave you the full refund (even though it would be obvious to a child that he should not have done so), and there has been no involvement of the courts or police, I do not expect that you will face charges.
If you feel bad that the store employs such an incompetent clerk, and want to go back to speak with a manager and try to get the credit corrected, I don't see that anything is stopping you.

