Hello Tim
Thank you for your help, this resolved some of the issues but we are still getting questions pulled into course level categories that seem to have been put into categories created at a system level. It appears to be probable that these categories were created while teachers had the permission to see/move/edit ALL categories. It also looks like part of the issue is that many of these courses affected were created from a common template.
I am starting to think I may need to manually remove the unwanted categories and questions but am still hoping I can find a way of doing so globally.