Can you double-check if references are activated in the workflow settings?
If references are structured in JATS XML, it’s possible to format them according to the preferred style in the output. See best practices according to JATS guidelines: https://jats.nlm.nih.gov/publishing/tag-library/1.3d1/element/element-citation.html
References are saved in OJS database, each separately, in raw format.
For now, OJS doesn’t allow to preserve citation structure, only raw reference. In means that if JATS XML contains info regarding authors, their surname and family name, article title, journal where article was published, etc., this info will be lost during conversion and it will be saved as a simple string. In near future I’m planning to change this behavior, this allows, e.g., export references in different formats (bib, ris…), supported by reference manager software, like Zotero or Mendeley.