Maybe wrong identification method was chosen. Let\’s say, you uploaded products using SKU as identifier, but changed SKU in your sheet, thus, Magento treats it as separate products. You you have chosen other identifier then SKU, lets say ID. I recommend to stick to chosen identification method.
In any case, you can re-import using Store Manager for Magento tool, which has the option to delete products which are not in .csv. In this way you will upload new correct products and delete existing ones including duplicates on the go.
There is 2-weeks free version of Store Manager tool, so you can download it and try out mentioned -
http://www.magentocommerce.com/magento-connect/store-manager-for-magento.html
