The reason you may be seeing Attendance duplicated could be 1 of 2 things.

1. Your Academic Terms are overlapping, to check this go to:

Core > School > Years & Terms > School Level  

If the Start Dates and End Dates of the Terms are the same you must change it so one term ends on one day and the other term starts on another day.

For example if your 1st Semester ends on 1/1 and your 2nd Semester Starts on 1/1 change the 1st Semester to end on 12/31.

2. Days to Default (which is creating a overlap of Terms) 

Days to Default should really only be used in the case where you have a gap between terms, such as a vacation.

Example if your 1st Semester ends on 12/15 and your 2nd Semester Starts on 1/1 you would want your days to default to be 17 to cover the gap between 1st Semester and the 2nd Semester.

Once you change the Default Days to 0 the duplicate Attendance should be removed.

You typically do not want to overlap any terms as this may cause other issues in other areas of the system.