As we all know, the latest Ubuntu release (Xenial) includes a newer GTK library than the old 14.04 (Trusty). This upgrade may (or may not, depending on your Ubuntu-derivated Distro) break some elements of the theme, notably sidebars and GNOME Headerbars / Titlebars. Here is an example of what could happen :
Thick and dark shadow and a messed sidebar are the consequences of an outdated codebase
So, how do we fix it? In short, all you have to do is add the code found in the appended file at the end of your theme's gtk-widgets.css file and it should work flawlessly from now on. Of course, be sure the colors used in the code correspond to those you use.