Dear Matthew Davies,
Good day to you!
I hope you are doing well. Thanks for reaching out to our Microsoft Community Forum. We will be happy to help you. Based on your description, I would suggest you wait for a while after adding student in class Team. Sometimes, it takes time to fully propagate. As well as add them via OneNote App to class notebook instead of Teams, and check whether you can see. I also recommend you remove the affected student and re-add that student. Generally, it may take some time to fully propagate. If the issue persists after a long time, I recommend you contact the administrator in your tenant and let him raise a service request. They have the expertise and resources to provide you with the assistance you need. For your convenience, I have attached the document: Get support - Microsoft 365 admin | Microsoft Learn.
I do apologize for any inconvenience. Thank you in advance for your understanding. Your patience and cooperation are greatly appreciated.Best Regards,Nahid Sultan