I am not really sure if it is a bug or a user error on my end. But I'm fairly certain that I do everything correctly.

Premisses / things known to work:

• Composite @NaturalId see HHH-11255 Closed
• @ManyToOne mapping with composite Primary Keys
• @ManyToOne mapping with @NaturalId

Expectation:
@ManyToOne mapping with non-primary embedded key (e.g. @NaturalId)

Example:

class Region {

    @NaturalId
    @Embedded
    private PostalCode postalCode;
}

@Embeddable 
@MappedSuperclass
class PostalCode {
    protected String countryCode;
    protected int zipCode;
}

class Town {
    @NaturalId
    @Embedded
    private TownCode townCode;

    @ManyToOne
    @JoinColumns(value = {
        @JoinColumn(name = "country_code", referencedColumnName = "country_code"),
        @JoinColumn(name = "zip_code", referencedColumnName = "zip_code")
    }
    private Region region;
}

class TownCode extends PostalCode {
    protected String town;    
}

Result:

Caused by: org.hibernate.AnnotationException: referencedColumnNames(country_code, zip_code) of Town.region referencing Region not mapped to a single property
	at org.hibernate.cfg.BinderHelper.createSyntheticPropertyReference(BinderHelper.java:321) ~[hibernate-core-5.2.17.Final.jar:5.2.17.Final]
	at org.hibernate.cfg.ToOneFkSecondPass.doSecondPass(ToOneFkSecondPass.java:101) ~[hibernate-core-5.2.17.Final.jar:5.2.17.Final]
    at org.hibernate.boot.internal.InFlightMetadataCollectorImpl.processEndOfQueue(InFlightMetadataCollectorImpl.java:1771) ~[hibernate-core-5.2.17.Final.jar:5.2.17.Final]
	at org.hibernate.boot.internal.InFlightMetadataCollectorImpl.processFkSecondPassesInOrder(InFlightMetadataCollectorImpl.java:1715) ~[hibernate-core-5.2.17.Final.jar:5.2.17.Final]

The error message sounds like I did a mistake. But I specified the mapped property via the @JoinColumns-Annotation. This mapping would work if it were a primary key.

Additionally it would probably be helpful if one could add the property/ies to map as a @ManyToOne parameter. But that probably will require an JPA API change if I understand this correctly.