Repository: unstable
GNOME Terminal version: 3.20.2
Default GTK theme

According to Ikey, the issue in the screenshot is caused by the transparency patches for gnome-terminal.
You can reproduce this by launching GNOME Terminal. Navigate to Edit > Profile preferences. In Profile preferences select the Colors tab. Under the Palette group click on one of the colors. You should see a window pop up with a transparent headerbar and buttons within it.