The cart icon appears below the menu in the Visual Builder

This is a quirk of the Visual Builder and is nothing to worry about. 

If you're using the Menu Module's Cart Icon, it may appear positioned below the Menu on it's own line within the Visual Builder. 

Here are two screenshots illustrating this: 

The Visual Builder Quirk with the icons below the menu text:

And the same header template displaying on the front-end:

Until this quirk is fixed in the Theme Builder, all you need to do is save your template and then view your header in the front-end and it will work perfectly.