In some resources, some of the References are missing. For example,  MedicationRequest has a CodeableReference to Medication and to Condition.

But Medication resource does not have the reference to "MedicationRequest" in the section where the resource is used, neither does Condition.
http://build.fhir.org/medication.html#11.5.2

This seems to be the case for other resources that are used in a CodeableReference.