To resolve this:
Academics > Grades > Grades Management > Enter Grades by Student, and remove all of the grades for one of the duplicated sections for that Student.
Academics > Scheduling > Requests and Schedules > Classes > Manage Sections, and drop the section grades were deleted from as a Scheduling Error. This will remove the course record.
To get the correct credits to display on the transcript you can:
Manually change the Credits Earned/Attempted via Academics > Grades > Grades Management > Enter Grades by Student
add the additional section as a transfer grade through Academics > Grades > Grades Management > Enter Grades by Student > Grades & Credits- Transfer > View > Edit.
The other option is to change the credits in Academics > Scheduling > Requests and Schedules > Departments & Courses > Course Title > adjust the credits to half the amount (if they were worth 1 they will now be worth .50)
Note: Editing the credits manually will cause the changes to reflect on the Transcript (this also changes historically for all users with credits from this course). For future years, it would be best to create duplicate courses if a student is going to be in 2 sections within the same term. Set the courses up as individual courses ex. Course A, Course B, Course C this way there are not duplicate credits created.