This can be:
A permission issue.
A caching issue.
If some section groups do not appear in the organisation structure the first step is to check that the permission to view the section groups is all assigned to the user, employee, role, or post that requires access.
If permissions are assigned
If permissions are assigned, follow the below steps:
In the Edit Permission screen, deselect one of the Section Group permissions.
Click Save.
Re-enter the edit permission screen and assign the View Permission
From within the Batch Updates menu option, Clear all user security cache.
Within Batch Updates, click Reload All Cache.
Return to the organisation structure and the section groups should now be visible.
If permissions are not assigned
In the Edit Permissions screen, select all section group view
permissions to the user, employee, role or post.
Select Batch Updates menu option, Clear all user security cache.
Click Reload All Cache.
Return to the organisation structure and the section groups should now be visible.