The template has the main menu controlled in the template settings. If you have main menu published in any module position which exist in the template, it will appear twice.
Depends in which one you want to use.
1- If you want to keep the horizontal main menu which is controlled in template settings do the following. In Joomla backend go in Extensions - Modules. There unpublished the module where you have the main menu.
2- If you don't want to use the horizontal menu, in Joomla backend go in Extensions -Templates. There click in the default template. In template parameters Menu tab you can select not to show the horizontal menu.