Let's perform some troubleshooting steps so the payments won't auto-apply to your open invoices.
Since the Automatically apply payments option is turned off, let's run the Verify and Rebuild Utility tools to check if it's a data issue. It's a good start when it comes to fixing data-related issues.
To run the Verify Data utility:
Click the File menu.
Click Verify Data.
If there are issues found, you’ll be prompted to RebuildNow.