The Features that are set up in Configuration, NetClassroom, Features are defined by school.  If only one school exists, then the Features apply to all students.  If you have a student who doesn't have a progression entry in the current academic year or in one of the other years selected to show in NetClassroom, then they aren't technically "in" a school and are not bound by the Features defined in Configuration.  Thus, they will see more Features than what's selected.  

If logging into NetClassroom as a new student or as the relation of a new student:
First check the dates of the upcoming academic year in Configuration.  If today's date is before the start date, then they will see all features.  The student and their relation(s) will see the appropriate features when the new academic year starts.  To change what they see prior to that start date, try one of the following: 
  1. Check the box for the year that hasn't begun yet in Configuration, NetClassroom, Grades and Years to Display
  2. Change the Start Date of the year that hasn't begun yet in Configuration, Academic Years
If logging into NetClassroom as a relation of a graduated student: 
Graduated students won't have a progression entry for the current or any upcoming academic year.  To prevent relations from seeing more features than what's defined in Configuration, unmark the View NetClassroom checkbox for that relationship on the Relationships tab on the graduated student's record.