If an invoice comes back queried from your referrer source, not only can you see the reason on the invoice within Pronto, but you can click on the View Invoice button displayed in the image below:
You will then be brought to your invoice on TM3. This will allow you to Edit, fix all the changed and then click Submit. The Submit and Edit Invoice buttons will be in the exact same position.
Once you have confirmed the changes and submitted the invoice, you will now see the referral has the new invoice submitted: