Several of our users have been confused by the fact that if you view and then edit a saved filter, edit the JQL that defines the filter (in Advanced mode) or change any custom field (in Simple mode) and then click the "Save as new filter" link that what will be saved is not the filter defined by the changes you just specified, but instead a copy of the original saved filter. A solution to this would be to gray out that link any time a query has been edited but the "Search" button has not yet been clicked.