Instances activity tells you how many courses have this enrollment method added to them. However, just because a course has an enrollment method added to the course doesn't mean that course is using the enrollment method.
For example, the Trends in Tourism course has three enrollment methods added to it:
Note in the preceding screenshot that while Guest access and Self enrolment are added to this course, they are not available, that is, they are not enabled. The teacher or administrator will need to enable those enrollment methods for this course.
Self-registration enables a person to join your site. Self-enrollment enables a person who is a member of the site to enroll in a course.
In this example, while we configured our site, we turned off guest access and self-registration for the site. However, those methods had already been added to this course; that's why those methods still appear in this course. They can be turned on for just this course, but they cannot be added to any new courses.
In Moodle, as in most systems, settings for a specific area override settings for a more general area. Many default settings that apply to your whole site can be overridden by settings in a specific course. Also, many settings that apply to a whole course can be overridden by settings in a specific activity.