I'm creating a web map in ArcGIS Online that references a MapServer from our internal server, which also has feature access enabled (FeatureServer) for editing. When I add both services to Web AppBuilder I get duplicate layers in the Layer List (one for each layer individually, plus the "group" layer that normally shows for the MapServer alone). Is there a way to display only the MapServer in the map and legend, but still allow feature editing through the FeatureServer?
Are you adding the map service and the feature service to the same web map? If you want feature editing you will need to have the feature service in the map. If you do not need bot services in the map I would remove the map service.
Hope this helps