If you click on the Link or Cite menu for the first time, you see a short explanation of what these functions do. While the explanation window is still open, if you mouse over a template at the top of the article, the blue highlight around the template appears in front of the explanation window. The template content itself is behind the window, as expected. The highlight should be behind the window as well, so that the window appears to be the front-most thing on the page.
This behaviour was observed in Chrome on Windows 7.