We just noticed a similar issue. Has there been any resolution to this?
A few subscription orders have been charged twice with a few days between the charges. The initial charge is recorded in WooCommerce as an order and in Authorize.Net. The second charge is only recorded in Authorize.Net and does not appear in WooCommerce. Additionally, The order number for the duplicated transaction is not in sequential order with the other orders (for example: the initial subscription charge is order #6118, appearing in Authorize.Net on Jan-08-2017, and is followed by order #6119, #6120, and so on, while the duplicate charge is order #5467, appearing in Authorize.Net a couple of days later on Jan-10-2017).
Please let us know of any additional details that may be needed to get to the root of the issue.