This assertion in the associated schematron files may be a bug:

<sch:assert test="not(exists(for $id in f:contained//f:id/@value return $contained[not(parent::/descendant::f:reference/@value=concat('#', $contained/*/id/@value) or descendant::f:reference[@value='#'])]))">dom-3: If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource</sch:assert>

Note- every .sch file that contains this assertion should be checked; the above this of Related Artifacts is not exhaustive, it's just all I have initially checked.