This is usually because the exception for already has taken the course is set to Show message.

If the Course Parameter Has Already Taken the Course is set to“Show Message” The User will get the following message:
Before continuing, please note the following:
You have already completed this course. If you are sure you still want to request it, click 'Confirm' to add it to your list of requests.
Note: The system does not lock the Course down and the Student can still select the Course.

To correct this navigate to:
  1. onRecord > Settings > Course Request Setup
  2. Select School Year, Group Type, and School Level
  3. Under Exceptions To Communicate Has Already Taken the Course there is a dropdown box where you change from show message to hide course from course list. This will no longer show the course to the student to be requested.