You would need to mark the course to exclude from transcripts/report cards.
For us to assist you further, would you please confirm if you have any stored grades for those sections? If yes then please exclude it as well.
Also would you please confirm if you are using report card or an object report?
In order to protect your privacy and avoid sharing of any Personal Identifiable Information (PII) data in the Community, we recommend reaching out to the Technical Support Contact of your district who should be able to connect with the PowerSchool SIS Support Team on your behalf. The Support Team should be able to take a closer look at your setup, gather more information regarding your issue, and assist you further with the troubleshooting steps.