There are two types of discounts: general discount and membership discount.
A general discount applies to a specific course. It is set in Advanced settings in the Pricing portlet:
A membership discount is a type of discount that applies to a specific user group, role, or organization.
For it to apply, a corresponding setting should be toggled in Advanced settings of a course (it is by default).
If a user has an overlap of membership discounts, the highest one will be applied.
You can also disable/enable all existing membership discounts at once, or toggle each one separately.
A general discount and membership discounts can be active at the same time - they will be summarized.