This is most often due to either Attendance records or Grades that have been entered for the course. The reasons can be viewed by hovering over the radio button when managing the student's enrollment in onRecord.
Scheduling error hover
Note: Hovering over Error in Academics > Scheduling > Requests and schedules > Set section info will not display the reason.

To remove Grades:
  1. Go to Academics > Grades > Grade management.
  2. Select Enter grades by student.
  3. Search for the student.
  4. Click View next to Grades and Credits.
  5. Click Edit.
  6. Remove any grades/credits/comments entered for the course.
  7. Click Save.
To remove Attendance entries:
  1. Go to Academics > People Finder.
  2. Search for and select the student.
  3. Select the Attendance tab.
  4. Expand the term in question.
  5. Locate any attendance entries for the class to remove.
  6. Click on the reason and change to Attended Class.
  7. Repeat for any additional entries/terms.