Normally, this shouldn’t happen. When you set subIndicators: false in “jquery.smartmenus.bootstrap.js”, the SmartMenus plugin will not generate any caret elements. So you either have 2 carets in source or maybe one of them is displayed via CSS generated content (i.e. some :before or :after rule) or some additional JS code that you use.
If you like, please post a link to some sort of live example and I will check it.