4
You can create a Unique field (Unique_Course_Student_Relationship__c) on the junction object and populate it with a concatenation of StudentId and CourseId through a workflow on create.
CASESAFEID(StudentId) + CASESAFEID(CourseId)
This will ensure that there's never two junction records with the same Student and Course as the value of that field needs to be ...
2
You can write a before trigger on the junction object and check if the combination already exists. If yes then use addError to throw an error.
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