Why was a wait list entry was charged
If one person is registering two people, but only one registration inventory item is available, both entries are charged at the time of payment.
ie - Eric Jr registered for both himself and his father and had both registrations in his shopping cart when he went to check out. Since the transaction isn't complete at the time he adds the 2nd registration (the one for his father) to his cart, inventory has not been updated, and we can't tell that there are not 2 spots available at the time of checkout.
So, when he went to check out, payment will processed for both registrations, even though one was waitlisted. This happens infrequently, and there is not a easy way around it. However, if you wanted to keep this happening in the future, you could set the max quantity to a lower level (39 instead of 40) and then manually move the people off the waitlist.