Are the CSV layers hosted in ArcGIS Online/Portal for ArcGIS? You mentioned that the CSV layers were added from a web location, so I suspect that's what is causing the issue at hand. According to our documentation:
"You can create filters on hosted feature layers, ArcGIS for Server feature service layers, and ArcGIS for Server map service layers that have associated attribute data. You cannot create filters on map notes or features imported from a file" (Apply filters—ArcGIS Online Help | Documentation ).
Hope that helps! Let me know if you're still encountering the issue, and I'll be happy to continue troubleshooting.
Just an idea. I wonder if it is possible to use Arcade to create a custom expression that changes unwanted item value to zero (or NULL). This could act as a pseudo-filter.