This may be a Mountain Lion thing, but maybe just my local issue. I currently have 4 instances of AC open, however, the Dock only shows 2 open. This make it a bit hard to close it down other than force quitting, and there you can't actually tell which one you want to close. I have cleaned permissions etc (via Onyx)
Running Mountain Lion here and no troubles with multiple instances of AC16 showing in the dock. It seems like there is something specific on your operating system. But it's tough to draw a conclusion at this point. If you wish to provide more details I would be happy to look into it further to see if it is something on our end that we can help with. If you would like to continue with this one on one you can send an e-mail to support@graphisoft.com.