You can ensure that discount codes are not applied in addition to already discounted items in 2 ways:
In Shopify admin
Creating a collection:
Create a new collection named "Eligible for Discount".
Under 'Collection type', choose 'Automated' and set the condition to include specific products. For instance, with the below conditions, you can include all products not on sale.
Product price is greater than 0.
Products where Compare at price is empty.
Updating discounts:
From your Shopify admin, go to 'Discounts'.
If you're creating a new discount, click 'Create discount'. To edit an existing one, select the discount from your list.
In the discount settings, under 'Applies to', select 'Specific collections'.
Choose the "Eligible for Discount" collection you created earlier.
Ouiteo's Ultimate Collection Manager
Creating a collection:
Create a new collection named "Eligible for Discount".
Under "Select what products to add" section, set the condition to include specific products. For instance, with the below conditions, you can include particular products not on sale.
Include either Product type or Vendor name.
Exclude Discount % is greater than 0.
Updating discounts:
To Update or create a new discount code on Shopify, refer to the steps outlined in the section Updating discounts of the article.