CTO of Goaffpro here. I cannot actually understand where the issue is as far as the app is concerned. Please help me out so we can help each other

As per the sent screenshots. You have set to
1. Give commission only for new customers (in the Settings page)
2. You have NOT checked the "Disable commission for self referral" OR "Disable commission for other affiliates" referral in the Settings page
3. You have NOT added the PARTNERS as the personal coupon to the affiliate

So, the rules of an affiliate getting a commission for the sale are
1. The customer should be a NEW customer
2. The customer should use the affiliate's link OR the affiliate's coupon code for placing the order

Now, in the order #1041, both the rules are satisfied.
i.e. the customer IS a new customer AND they used the affiliate's link to place the order.

As a technical person yourself, you can understand writing something in the terms and conditions or verbally mentioning this to the affiliate will not actually tell the app anything. You will have to set the appropriate settings there as well. For this reason, we have an exhausting documentation here
https://docs.goaffpro.com
and tons of videos here
https://www.youtube.com/channel/UCo95DNTq0v3WDjqECo3eKWQ?view_as=subscriber

(Just like you cannot just write something in the terms and conditions in your shopify store terms page, you actually have to set the rules/prices/charges/taxations etc in shopify as well)

Though as far as I checked, nothing like this was stated in your signup page terms or the actual terms and conditions page. i.e. It is nowhere stated that they will NOT receive commission for personal orders.

Simply put, you just had to add the coupon PARTNERS as their personal coupon AND optionally Tick the "Disable commission for self referral" in the Settings -> General Settings tab and the sale would not have given the affiliate any commission

With regards to your second query, If you notice there is a "Also create in store" checkbox in the popup. This option works with the automatic personal coupons in the Coupons page. So if you have set the "Automatic Personal coupons" in the Coupons page -> the app will create/manage the personal codes. OR you can simply just UNCHECK the "Also create in store" option and assign the code to the affiliate yourself.

To inform your affiliates that they will NOT receive commission for their personal orders or for usage of personal coupon code, you can use the options below
1. Send them email telling them of change of policies of the program (Use the Bulk Mail option in the sidebar)
2. Write the appropriate terms in the Signup page, see screenshot below
3. For existing affiliates, you can also write this in their dashboard via Look & Feel -> Affiliate Dashboard tab -> Extras instructions section

Finally, I personally apologize for any troubles this may have caused.

Hoping for a fruitful discussion so we can maintain the cordial relations and grow together. Your success is our success.