We are using SharePoint online. I have a sub site called grants which has a group called Grants Owners. I have give Grants Owners Full Control. In Grants there are several document libraries. It appears that those who are in the Grants Owners group can not see all of the folders in the document library. Do I have set any permissions at the root level or just at the sub site level?
If that document library lives in the sub site then permissions to only the sub site should work. Check to see if there are unique permissions on the document library itself or any of those folders they are not seeing.