Via T247922: Display parent references of subreferences in the VE pop up and wizard we made the parent-child relationship between Cite-Extends references visible everywhere in VisualEditor, with one exception: A short <ref name=x/> can actually be a sub-reference. But we only know that after we resolved the name. The current code doesn't do this but assumes an extends=y attribute is there.
Example wikitext to play around with:
A<ref extends=book name=p20>p. 20</ref> B<ref name=p20 /> C<ref extends=book name=p20 /> <references> <ref name=book>book</ref> </references>
The bug here is that the second reference will not show the parent in the ContextItem popup and in the dialog.
Note you can easily run into T367749: Can't reuse an extended reference by name before it is defined when you play around with this example. While the two are related they really are separate issues.