Just looking at the screenshot, my best guess is that you've unknowingly upgraded your system to a newer version of Gtk+ that is incompatible with the elementary stylesheet. This makes Builder work, but it might cause issues with other apps.
To check which version of Gtk+ you have installed, you can run the Terminal command:
sudo apt-cache policy libgtk-3-0
You should see some output like:
*** 3.18.9-1ubuntu3.1 500
500 http://us.archive.ubuntu.com/ubuntu xenial-updates/main amd64 Packages
500 http://us.archive.ubuntu.com/ubuntu xenial/main amd64 Packages
This tells me that I have version
3.18.9 installed. This is the original version that ships with elementary OS.
If you have a newer version of Gtk+ (like
3.20), you can either try to manually edit the stylesheet to fix issues yourself, switch to a stylesheet that supports whatever version of Gtk+ you've upgraded to, or try downgrading Gtk+ to the original version shipped with elementary OS.