The problem is apathy, not incompetence. The site (or more accurately, the middleware powering the site) was probably built for IE5/6, which was not at all uncommon ten years ago when "everyone" (not literally, but I know you know what I mean) had IE. The software did the job for so long that the people in government let it run and turned a deaf ear to the distress it caused for constituents. It's easier to tell constituents to go find IE9 than to upgrade the system. They also fall into the "the perfect is the enemy of the good" trap, telling themselves that they don't need to just fix the IE problem, but they need to totally modernize the whole system including the backend and business process.
If the government had a magic button that could fix the problem, they probably would have pressed it. But no such button exists (unless you count injecting the X-UA-compatible tag), and modernizing the system is a lot more cost and effort than that.