Hello there, condowb.
QuickBooks only accepts information from the Bank. It's possible that your bank posted the invoice payments as an outgoing payment that's why it appears the same way in QuickBooks.
Let's perform some steps to resolve this.
Let's exclude these transactions. Then, you can manually upload them in QuickBooks.
To do this, you can go to your Bank's website and download the the affected transactions in a file format which QuickBooks Online support.
You can use any of these file formats:
Once done, you can manually upload them in QuickBooks Online by using the WebConnect feature.
Don't hesitate to post again if you have further questions. Have a good one!