Try each of the following steps in order until the issue is resolved:

1.  If using a static query, refresh the query.

2.  Re-print the query control report.

3.  Remove all output from the Query and check the results.  If there were duplicates removing the output should prevent the duplicates from occurring.  

Note: The query list counts lines in the results, rather than counting the number of records, and may contain duplicates. The query control report counts records and does not include duplicates.