Managing Folder/Document Permissions avoiding access denied on Site Page

Hi,

Let me laying things out

Office 365 Sharepoint Scenario:
Sharepoint Enterprise E3
No other Servers/Active Directory/Azure are involved, 100% cloud based
Single site collection: Company-SPS
Site Collection Features Enabled (Active)
- Disposition Approval Workflow
- Document Sets
- Library and Folder Based Retention
- Reporting
- SharePoint Server Enterprise Site Collection features
- SharePoint Server Standard Site Collection features
- Site Policy
- Three-state workflow
- Video and Rich Media
- Workflows

This collection has Subsites setup per department:

- Accounts
- Human Resources
- Sales
- Health and Safety

What we end up with is the following websites:

- Company-SPS Sharepoint Site: *removed*.sharepoint.com/SitePages/Home.aspx
- Company-SPS Accounts Sharepoint Sub-site: *removed*.sharepoint.com/accounts/SitePages/Home.aspx
- Company-SPS Human Resources Sharepoint Sub-site: *removed*.sharepoint.com/humanresources/SitePages/Home.aspx
- Company-SPS Sales Sharepoint Sub-site: *removed*.sharepoint.com/sales/SitePages/Home.aspx
- Company-SPS Health and Safety Sharepoint Sub-site: *removed*.sharepoint.com/healthandsafety/SitePages/Home.aspx

What we have is one link that is provided to all employee's to the Company-SPS Sharepoint site (view only), we've given them access to this to simply access the list of Departmental Subsites. At present, the employees ONLY have access to the Subsites (Accounts, Human Resources for example) that they have been invited/granted permission to by stopping inheritance. Our employee's use the 'Following' feature as a shortcut from their Sharepoint landing page to get to the respective Document Library of their Departmental Subsite. This is really the only collection feature we use at the moment and have uploaded our files to the respective Departmental Subsite/s.

The Issue
As we are working mainly in a browser environment it's important our employees have a flowing experience from the word go, this includes navigating to the Company-SPS Sharepoint Site: *removed*.sharepoint.com/SitePages/Home.aspx or Signing into Office 365 & selecting Sharepoint and using the 'Following' shortcuts they have made but, problems in that flow arise when within the department subsite document library an employee is allowed access to only one folder, they cannot access the subsite via 'Following' link,

At present we have an example employee who can access the:
Company-SPS Sharepoint Site: *removed*.sharepoint.com/SitePages/Home.aspx

That cannot access their departmental subsite via:
Company-SPS Accounts Sharepoint Sub-site: *removed*.sharepoint.com/accounts/SitePages/Home.aspx

But can access the folder shared via a link from sharing:
*removed*.sharepoint.com/accounts/Shared%20Documents/Forms/AllItems.aspx?newTargetListUrl=%2Faccounts%2FShared%20Documents&viewpath=%2Faccounts%2FShared%20Documents%2FForms%2FAllItems%2Easpx&id=%2Faccounts%2FShared%20Documents%2FBookings

And even access the documents list directly from:
*removed*.sharepoint.com/accounts/Shared%20Documents/Forms/AllItems.aspx

How can I maintain the flow here for the employee, granting them access to just the Home page of Accounts and not access to the rest of the folders?


Any idea's or advice would be greatly appreciated :)