In admin/cron.php, when we "Delete users who haven't completed profile within required period" (as described in the comment), we use get_users_not_fully_set_up function, but in the administration page this option is described as: Delete unconfirmed users after X days.
In general a not fully set up user even if confirmed, we'll be deleted. This is an unexpected result for Moodle's administrators because unconfirmed hasn't the same meaning of fully set up.
I suggest to use get_users_unconfirmed instead of get_users_not_fully_set_up. On the contrary I hope get_users_not_fully_set_up will be extended to work also with all required custom user profile fields when you try to login.