When creating a web app from a web map, data from a CSV file imported directly to ArcGIS Online Map Viewer do not appear as a layer selection in the Web AppBuilder for ArcGIS Filter widget.
The image below does not show any layer when configuring the Filter widget, although the imported data from the CSV file are displayed on the map.
This is by design. Only hosted feature layers can be filtered, queried, and edited. So, the Filter widget only shows hosted feature layers as its selection. For more information, refer to ArcGIS Online: Apply filters.
To ensure the layer selections are available for the Filter widget, publish the CSV files as hosted feature layers. For more information on publishing hosted feature layers, refer to ArcGIS Online: Publish hosted feature layers. This also applies to filtering in ArcGIS Online Map Viewer where the Filter icon is disabled when the layer is not hosted in ArcGIS Online. For more information, refer to FAQ: Is there a way to apply a filter after importing a feature from a file to ArcGIS Online?
Note: Only users with Administrator and Publisher roles are able to publish hosted feature layers.
The image below shows the hosted feature layer is displayed as a layer selection in the Filter widget after the CSV file is published.