One course counts toward two graduation requirements because each requirement counts every course its course requirement matches, so a course that matches both counts in full toward both. This sharing is the default on every graduation plan, and it suits a course that meets two requirements at once, such as a course on Indigenous history that counts for both Social Studies and an Indigenous Studies requirement.
When the course should count toward only one of them, add a credit link between the two requirements on Administrator > Maintenance > Graduation Requirements. The course then counts at the requirement in Takes Extra Credit From, and it reaches the requirement in Counts Toward only as credit beyond the first requirement's target. Review Creating Graduation Requirement Credit Link.
The course requirements can also be narrowed so that only one of them matches the course, for example by course type and level. Review Creating Course Requirement.
Note: Adding a credit link changes the numbers as soon as it is saved, on transcripts for past school years too. Review Graduation Requirement Credit Counting.