I've recently had two customers charged twice with two orders produced. The last customer has suggested a possible cause.
She inputted her credit card details (PayPal Pro for osCommerce 2.2MS2+) and clicked to proceed but she had not clicked on the radio for credit card.
The card returned an error saying no payment method chosen. She then of course tried again with it chosen.
This may or may not be the cause but she was charged twice and two orders generated.