This solution article is to explain what this error means.

In your submission to the ministry the classes that are taught in the Same Semester, Same Period, Same Teacher, same room are grouped together so that the Average Class Size Report shows proper class sizes.  

In your next submission to the ministry one or more of the classes grouped within now have zero students enrolled in the class and due to the fact that the ministry does not want zero occupancy classes it tries to delete it, but as you know because the class was already sent up with a student enrolled in the previous submission it cannot delete it as it must send up the mark and credit to complete the class if the student completed it or drop it if the student did not complete it.