gistfile1.java

    @Test
    public void shouldDeleteOnePatient(){
        deleteAndPopulateTables("doctors", "patients", "doctors_patients");
        Doctor doctor = Doctor.findById(1);
        List<Patient> patients = doctor.getAll(Patient.class);
        a(2).shouldBeEqual(patients.size());
        doctor.remove(patients.get(0));
        patients = doctor.getAll(Patient.class);
        a(1).shouldBeEqual(patients.size());
    }

Another option would be to delete an entry in the join table by using the model of the join table.
Then both @Cache statements for Doctor and Patient could stay there :-)

@rivella50, the cached annotations works in such a way that in case, that whenever there is a destructive call like delete something, the framework will drop all associated caches. In this case, it will drop caches for all three tables. The test I wrote above is working as expected, so there must be something in your code. Are you using include() method when loading?

Not anymore!
I will try to create a test class which should demonstrate what is not working correctly.
I'll post the code here when i'm ready