Thank you for the detailed information, @OlAl.

Usually, invoices won't automatically be paid or applied for the existing credits when the Automatically apply credits feature was turned off from the Account and Settings. 

In your case, you can try using a private window to replicate the process. Sometimes the regular browser tends to hold into information and over time can cause problems while working with QuickBooks. To save you time, use either of these keyboard shortcuts:

• Mozilla Firefox: press Ctrl + Shift + P
• Internet Explorer: press Ctrl + Shift + P
• Safari: press Command + Shift +N

If that works fine using a private browser, go back to your original browser and clear its cache to start fresh as suggested by MorganB above. Also, using other supported browsers can help us narrow the cause of this behavior.

If the problem continues, let's try deleting and recreating the transactions after turning off the automation of applying credits to invoices. This helps us narrow down the cause of this unexpected behavior.

Update me with the result by adding a comment below. I'm always here to help however I can. Have a good day!