Use Running Totals instead of Summaries to obtain the subtotals as they are more flexible and give accurate results.

If you must use a summary field and the summary field is duplicating the counts/totals, select "Select Distinct Records" under File/Report Options.

Cross tab reports can sometimes cause duplication in the rest of the report which can result in incorrect Summary totals.  If you do have Cross tab reports, move them to a subreport.