We have found several cases where customers are being charged for multiple transactions with the same invoice numbers. However, only one of the transactions actually shows in Magento. The other transactions appear to be duplicates that Magento did not process, but authorize.net still created successful transactions and processed payment.
It seems that Magento is trying to reuse existing order numbers so this causes the order not to be processed in Magento, but it still goes through in authorize.net.
This does not happen with every order and it occurs with both customers who check out as guests and customers who are logged in registered users. We are currently using version 2.0.7.
We have have the same problem. Have you received an answer from anywhere?