Message Title

Well, I checked your test case and tried to "simulate" what Springs JtaTransactionManager.triggerBeforeCompletion() is doing. I added entityManager.close(); before the transaction is going to be commited to you test case and could reproduce the issue against Hibernate 5.3.1.Final.

According to Jürgen Höllers comment at https://jira.spring.io/browse/SPR-15334, the "closed" or "opened" state in JPA is a user-level indication. However, the underlying session should be able to participate in the transaction commit phase even if the entity manager is closed for user interaction.

    @Test
    public void addRelationImplicitFlush() throws Exception {

        Long contractId = doInJPA( this::entityManagerFactory, entityManager -> {
            Contract contract = new Contract();

            entityManager.persist( contract );
            return contract.getId();
        } );

        Long customerId = doInJPA( this::entityManagerFactory, entityManager -> {
            Customer customer = new Customer();

            entityManager.persist( customer );
            return customer.getId();
        } );

        doInJPA( this::entityManagerFactory, entityManager -> {

            Customer customer = entityManager.createQuery(
                    "SELECT c " +
                            "FROM Customer c " +
                            " LEFT JOIN FETCH c.contractRelations " +
                            " WHERE c.id = :customerId", Customer.class )
                    .setParameter( "customerId", customerId )
                    .getSingleResult();

            CustomerContractRelation relation = new CustomerContractRelation();
            relation.setContractId( contractId );
            customer.addContractRelation( relation );

            // simulating spring JtaTransactionManager.triggerBeforeCompletion()
            entityManager.close();
        } );
    }