All discounts assigned through an upsell create a discount in your store.
This means that if you're using a trigger upsell, ANYTIME a customer has both the trigger product and the upsell product in their cart, it will apply this discount — regardless of if they added the product through the upsell or not.
It also means that if you applied this discount through a catch-all upsell, this product will automatically be discounted on your store when it appears in a cart, regardless if they added from an upsell or not.
To avoid this, in any case, simply follow these instructions.
WHY DOES THIS HAPPEN?
We are limited to the way BigCommerce is configured and our only option to allow you to apply discounts is to auto-create on in your BC store.