EntityNotFoundException on save for wrong composition

Question

I found weird Hibernate behavior that I can not understand.

Let's say I have class A (was inspired with this question JPA: How to have one-to-many relation of the same Entity type)

@Entity
public class A {

    @Id
    private String id;

    private String name;

    @ManyToOne
    @JoinColumn(name = "PARENT")
    private A parent;

    @OneToMany(mappedBy = "parent",cascade = { CascadeType.PERSIST, CascadeType.MERGE, CascadeType.REMOVE })
    private Set<A> children;

    // Getters, Setters, etc...
}

Also, say we have Spring JPA Repository

public interface ARepository extends JpaRepository<A, Long> {}

And test class where magic happens

@RunWith(SpringJUnit4ClassRunner.class)
@ContextConfiguration({ "classpath:spring/applicationContext-test.xml" })
public class ATest {

    @Autowired
    private ARepository aRepository;

    @Test
    public void testA() {
        A parent = new A();
        parent.setName("I am Parent: 121_1001_21");
        parent.setId("121_1001_21");

        A son = new A();
        son.setName("I am Son: 121_1001_31");
        son.setId("121_1001_31");
        son.setParent(parent);

        A daughter = new A();
        daughter.setName("I am Daughter: 121_1001_32");
        daughter.setId("121_1001_32");
        daughter.setParent(son);
        // daughter.setParent(parent);// yes, I'm intentionally creates wrong hierarchy

        parent.setChildren(new HashSet<>(Arrays.asList(daughter, son)));// order of elements in set matters!

        son.setChildren(new HashSet<>(Arrays.asList(daughter)));

        aRepository.save(parent);
    }    
}

So the hierarchy is following:

Parent (121_1001_21) 
  Son (121_1001_31) 
    Daughter (121_1001_32) 
  Daughter (121_1001_32) 

But this test fails on saving entity with

javax.persistence.EntityNotFoundException: 
Unable to find com.orga.pcom.om.core.entity.productorder.A with id 121_1001_31

After hours of debugging I found that Hibernates tries to load linked entities and load it in this way:

Parent (121_1001_21) 1st load
  Son (121_1001_31) 3rd load (this entity loading is fail!)
    Daughter (121_1001_32) 2nd load
  Daughter (121_1001_32) 2nd load

and fails! So, the questions are:

1. Why Hibernate loads something while it saves something? :)
2. What is the best way to fix this issue?