I've built a web map that has three layers (featured layers (hosted on AGOL). I then used the WebApp builder to create a Web App from the foldable theme. To this I have added the Group Filter widget and I've added three filter groups. When I launch the App, the filter groups work fine with only these three layers. I also need to add some other WMS layers from a Canadian Provincial website ( BC Data Catalogue). I add these to the map and then launch the web App again and the Group Filter groups are no longer available and I can no longer apply the filters. Is this expected behaviour? I can't find anything about this in the descriptions of the widgets.
Thank you!!! I had the same issue happen to me (using Portal 10.5.1), and after removing the WMS layers the Group FIlter now works!
Obviously this is a bug, but at least now my Group Filter works again.