The Natural HR organisation chart is very strict on company structure. The logic behind this is that, in a hierarchy, only the top of the pyramid should have no manager. 

If there is more than one employee with no manager, the org chart cannot know which employee is the top of the pyramid. 

When adding a new employee, ensure you choose 'Employee has no manager' only once.

For all other employees, ensure they are assigned to their correct manager as this can cause issues especially for reporting and manager approval for time off, expenses etc.