Yep, it's annoying. I have a few like you that I added manually and some of them are fine, and some will come and go (right now I have two that are the fugly icon, and on the next reboot they could be back or better, have a couple of more with the fugly icon).
And the truly idiotic thing about it is if I copy/paste or drag and drop the one(s) that are acting up, once they are on the desktop the game's regular icon appears.