Only items permanently pinned to the task bar exhibit this behavior. Pinning an item to the task bar (where running applications are displayed) just keeps its icon there permanently. On the other hand, in the start menu (perhaps similar to the activity menu? I haven't used Gnome3 with this new set up, yet.) even the pinned and recently used items, when clicked, open a new application.
Perhaps I misunderstood what the OP had an issue with. I perceived it as, when you attempt to run an application from a large, collective menu of all applications, if an instance is running, it would go to that instance, instead of starting a new one. This is not the way it is in Windows.*
If the OP declared that clicking a running application opened the running application, then yes, that has been the way it is for a while now, but it was that way in Gnome2, so I suspect this is not the case.
Only items permanently pinned to the task bar exhibit this behavior. Pinning an item to the task bar (where running applications are displayed) just keeps its icon there permanently. On the other hand, in the start menu (perhaps similar to the activity menu? I haven't used Gnome3 with this new set up, yet.) even the pinned and recently used items, when clicked, open a new application.