See w3c/epubcheck#1085

It appears that href attributes anywhere in the package file must be IRIs.

Each item element in the manifest identifies a Publication Resource by the IRI [RFC3987] provided in its href attribute. The IRI MAY be absolute or relative. In the case of relative IRIs, Reading Systems MUST use the IRI of the Package Document as the base when resolving these to absolute IRIs. The resulting absolute IRI MUST be unique within the manifest scope.

But we don't appear to forbid fragment identifiers. All we say about href is

An absolute or relative IRI reference [RFC3987] to a resource.

EPUBCheck complains loudly about fragment identifiers, I think because it misinterprets them as incorrect file extensions.

I'm not sure if we need to do anything here.