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I'm pretty sure that situations like below cause it:
Site
@ManyToOne(cascade = CascadeType.ALL, optional = true, fetch = FetchType.LAZY)
@JoinColumn(name = "DEFAULT_PAYMENT_OPTION_ID")
protected PaymentOption defaultPaymentOption;
SubSite extends Site
@OneToMany(fetch = FetchType.LAZY, cascade = CascadeType.ALL, mappedBy = "site")
@Cascade({org.hibernate.annotations.CascadeType.ALL})
private Set<PaymentOption> paymentOptions;
PaymentOption
@ManyToOne(optional = true, fetch = FetchType.LAZY)
@JoinColumn(name = "SITE_ID", nullable = true)
private Site site;
Note: PaymentOption has a reference to Site but a subclass of Site (SubSite) has the reference to PaymentOption. I think hibernate generates foreign keys for both sides but they get different names.
I don't have time to setup a test case for this but a structure like above should generate the problem.
Regardless, the test case that I did write clearly shows that the code wasn't working and that once fixed works as expected. As far as unit tests go, what I provided is better than a mapping file (for testing the code in question).