Hi @james_whalley,
Are you (a) cross-listing or (b) do you have a single course shell with multiple sections in it?
I am asking because my institution does not cross-list but we do have courses with multiples section in them and we have not had this problem reported and I am not able to duplicate when I try (while as an admin or an instructor).
When you go into "Course Analytics" and then to "Students", what do you see in the dropdown box above the list of students? Do you see the sections in the list to pick from? Do you see all of the students?
Are all of the students listed in the main porton of the page?
This might need to be reported to Instructure/Canvas Support for investigation, explanation, and resolution.
-Doug