You have to "tell" the where clause that the zone is in the subsidiary table:
Company.where(id_category: filter_categorys).joins(:subsidiary).where(subsidiary: { zone: 'Nuñez' }
If it says "relation subsidiary was not found", try with:
Company.where(id_category: filter_categorys).joins(:subsidiary).where(tbl_subsidiaries: { zone: 'Nuñez' }