Duplicate Attendance

Recently we have discovered that a small number of our students seemed to have a large number of absences (we record meeting attendance). We discovered that their attendance is duplicating in certain classes. The teacher takes attendance once during the block - sometimes at the beginning, sometimes in the second half - but always only once for the period. We have the sections set to take attendance once for the whole 80 minute block although some teachers may divide the block into two. Why all of a sudden, and why just a few students is this happening? How do we correct the issue?