Hi Ezpz, 

Thank you for the clarification. We have a few customer reporting similar experience with applying payment on invoices. So that we can better assist you on this, I would encourage you to contact our support team directly so they can look into this with you. Here is how:

https://help.quickbooks.intuit.com/en_AU/contact

Please let us know if you require additional assistance or have any question after contacting our support team. Thank you.