The reason leading to a double charge is when there is an active Payment subscription (Paypal or 2checkout) and a manual Payment was made prior to the subscription payment date.
A subscription consists in scheduling a payment to be sent at the specific date. At of this stage, there isn't any way for us to block such behavior of the payment being made since we aren't requesting the payment and it is being sent automatically from either your Paypal account or from 2checkout. You may manage your subscription from the respective payment gateways in their settings.
All duplicate payments are instantly detected and recorded by our billing platform and is automatically being added as Credit. Such Credit is an immuable billing record which may be used at any point of time for any other invoices for the current service or any other. You may enable / disable the automatic credit usage for your invoice from your client area in the invoice section.
Also, Overpayments can be refunded on the source payment gateway within the next 180 days following the payment date (assuming the funds weren't used on any invoices) and therefore aren't subject to 30 Days Moneyback guarantee limited terms.
In order to claim such refund, you would simply need to open a support ticket at the Billing Center stating the invoice / services overpaid and we will issue a refund.