Any members other than "$ref" in a JSON Reference object SHALL be
ignored.
We (JSON Schema) later bundled the separate JSON Ref specification into the JSON Schema specification.
As of draft 2019-09, $ref can be used alongside other keywords without this adverse effect, however this schema and many others in this repo use draft-04, and so may have instances validate successfully unexpectidly.
I raised this same issue at https://github.com/GSA/project-open-data-dashboard/issues/366 but thought it might be worth cross referencing, as you seem to use the same JSON Schemas for validation.
Regarding the catalogue schema...