In order for us to help you will need to tell us what kind of query you are running (constituent, gift) etc. and what the criteria is. 

They are not duplicate entries if they are different people.  True duplicates would be a different issue.

It is likely due to spouses having their own record and being soft credited for gifts and running your query on a SC to both option but without the criteria I can not say for sure.

What are you going to use the query for?  If for a mailing, then in export or mail options you would simply choose mail to HOH and this should not be an issue.  You would never export from query to do a mailing.