It seems that you have used the one page navigation incorrectly. You are supposed to create two sets of menu item. In the first menu, the item will have the menu items absolute path in the links like "http://example.com#section-ID". This will be assigned as your primary menu. And in your second menu, you will only have to link to a relative path like
#section-ID and this menu will be assigned as your one page navigation menu which will be used exclusively for the homepage. For more details how you can properly set up the one page navigation, please check this out: https://theme.co/apex/forum/t/features-how-to-setup-one-page-navigation/96/1
By the way, I noticed that you are using an older version of the theme and Cornerstone. Please be advised that we have released X 6.1.6 and Cornerstone 3.1.6. It is now available in automatic updates. You can now update to this latest version. This latest release contains fixes for several issues so be sure to check out the changelog (http://theme.co/changelog/).
After doing the updates, always remember to clear all caches (if you are using WP Rocket, WP SuperCache or W3 Total Cache) when updating so that the code from the latest release is always in use. This will help you to avoid any potential errors.
Hope this helps. Please let us know how it goes.