[after Suzanne contacting by email, on version 2.4.16.1]
Sorry Suzanne but I've followed your screenshots and set this up on 2.4.16.1 and 2.5.9 and it all just works, and I see all the users I would expect to see. And I can't see anything in the code that would exclude users based on the time of their manager assignment.
I notice you are using Organisation restrictions plus the Direct Reports restrictions plus the Future restriction. Is there an issue where some users have the manager set but are still in a different branch of the Org tree and that is why the manager cannot see them in the report? Or indeed the other way around where the users are in the right branch of the tree but are not assigned to the manager.I'm not sure what to advise at this stage because if the users and managers and report are all set up OK it just seems to work for me.