Are you asking about the limits that occur within academic freedom?
The important thing about academic freedom is that the limits are self-determined by appropriately placed scholars with the appropriate expertise themselves. For instance, I have a department of psychology that is accredited to offer degrees in clinical psychology. It is clinical psychologists across the country who determine what the accreditation standards are. They draw on their scholarship to do so, and then psychology departments across the country respect those accreditation standards in their curricula.