The fact that the header on the home page overlays the Shopping Experience is not a bug, but a configurable effect of ThemeWare® to provide a particular look in themes such as ThemeWare® Exquisite, ThemeWare® Lights or ThemeWare® Outdoor.
You are probably using one of these themes, because the ThemeWare® Shopping Experience Header is already pre-configured in them.
The following article explains how you can use or deactivate this effect:
Configuring the Shopping Experiences Header