I have the same issue, although I had set OFF Automatically Apply Credits, at the beginning, I can record the overpaid amount as QB showed "Amount to credit" but after I applied the Credit to other Invoices, QBO  automatically takes that Credit applies for wrong Invoices. I came back to the date I recorded overpaid and I didn't see anything that I did before (didn't see the Amount to credit). 

Is there any way to keep it manually apply and don't automatically change?

Thank you.