When publishing a clipped feature class as a geoprocessing service in ArcMap 10.5, there is no warning that the data will be copied to the server when the Analyze button is clicked in Service Editor.
Not reproducible. This sounds like an issue with understanding ArcGIS Server data source registration.
http://server.arcgis.com/en/server/latest/publish-services/windows/overview-register-data-with-arcgis-server.htm