It's all in the title.
Eg. if I have a gnome-terminal opened and I click on the gnome-terminal launcher icon, the running terminal will focus and no new instance will pop-up. Also, there is no item in the launcher icon's quicklist that would allow me to start a second instance of the program.
You now can start a new instance via a middle clicking on the launcher icon.
Click the launcher with the middle mousebutton.
At the moment, the only possibility to start a second instance, is using the Applications view, in the sidebar or the Ubuntulogo at the top.
If you want a second Instance of the terminal you must select "New Terminal" in the File Menu from gnome-terminal. It's similar with Nautilus. But (currently) it's not possible to start more than one instance from the Launcher
cntrl shift N opens a 2nd terminal where I have a terminal focused and cntrl D closes a termimal
Right-click on it's running launcher icon and choose New Window.