I am not sure if there is a limit to the number of layers that you can use a group filter on. In my current configuration of the widget I have about 45 layers that I am trying to filter on. They all have a common field in them. When I try to run the filter, arcgis online sort of freezes and the filter never runs. When I zoom in on the layers after running the filter, they do not redraw and just remain stuck/frozen. If I reconfigure the widget to only filter on about 15 layers at a time, then it works, although a bit slowly.