Automation is actually easy and I have no idea how they managed this mistake unless they were using a 3rd party (ie. non-MS) tool to deploy the update. We use WSUS and don't EVER have this problem because WSUS works with Windows Update specifically to install only what's applicable to that OS (System Center does the same thing but is more complex and has more features) - and includes updates for all MS products (so I can apply SQL updates along with Windows updates and minimize downtime for everyone and then only have one reboot - all without having to pay it any attention). When done properly automated update maintenance works great - I know it saves me a lot of time and manual labor.