SharePoint Permission and folder problem - even though the permission are given for them accordingly

Tariq_HR
Hi All,
I am working for a company in the HR department in the middle east.
Recently we developed a document management system on SharePoint. We have a diversified company with many departments and divisions. We had given permission to certain people in HR to access the folders of different departments and on top of that we had created a automatic system to make applicant folders which were converted to employee folders once the admin work was finished and the applicant was given an employee number in the oracle system.
The problem we are facing is that people who have permission to certain department folder are sometimes not able to send files or access the employee folders. Sometimes when the applicant is created the people who have access to that department folders cannot see the folders in the SharePoint application. However, the super user can access the folder in any case.
Can someone shed light on what is happening, the SharePoint system is working fine and folders are being created which can be seen only by the super user, but other users are having problems while accessing new employee folders or in other cases existing employee folders even though the permission are given for them accordingly.
Many Thanks
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