I'm guessing it's because he has multiple versions of the software installed. So if he has version 3.0.0 open and then clicks on his dock icon which points to version 3.0.1, it will open a second instance of the program.
Just so you know, when you install a new version of S3D, it will automatically go into a new folder so that it doesn't overwrite all of your old files. This is very convenient, because if something ever goes wrong with the upgrade, you can always go back to the old version. So if you open a Finder window and go to Applications, you will probably see several Simplify3D directories. If you are happy with the latest version, then you can just uninstall all of the old ones (go into the folder and run the uninstaller). Then just make sure that the shortcut on your dock points to the latest version and not one of the old ones.