General Workflow

For 3D Secure payments, the payment status first goes to 46. At this time, the invoice in Magento will be created, which is correct. Note however that the invoice status is "pending" as long as the payment has not been confirmed. The order will be in status "payment review" at this time.

As soon as the payment status changes to 9 (meaning the payment has been confirmed), the order status will go to "processing" and the invoice status changes to "paid". Information regarding this can also be found in the official documentation, section "Ogone/Magento status mapping".

If you don't want the invoice to be created immediately, you can switch from "Direct Sale" to "Authorization" in Magento. Then the invoice will only be created when you trigger the capture, in other words: click on "Invoice" in Magento and then select "Capture online".