Hi,
You can choose which one of the duplicate SEF URLs will be used by setting it as Active in the JoomSEF's URLs Manager.
You can stop generating some URLs based on a regular expression pattern. You can set it for individual extensions in JoomSEF in their Common parameters in "Do not SEF URLs matching regular expression" field.
Please post some examples of the duplicated SEF URLs and their corresponding Real URLs from JoomSEF's URLs Manager, so I can see what can be done about them.