In the developer portal on PayPal, can you get the two(or so) related API call logs for this transaction (event logs > api calls). - Feel free to send them via PM.
The exception is something we need to look into, but I don't see how a payment could be processed twice. With PayPal, the customer has to click a button to redirect to PayPal, then they have to sign in and then they have to click another button to confirm the purchase.