I receive this error whenever I run my extraction from the command line, not in the Spoon UI.
Missing plugins found while loading a transformation
Step : Mo
Having the MongoDB plugin as a dependency only works for compilation. When PDI runs it looks for a plugins/ folder under the current directory, and will load all plugins from there. You can override the location by setting the KETTLE_PLUGIN_BASE_FOLDERS system property. Either way, you'll want a plugins/ folder and to unzip the MongoDB plugin package (not the JAR) into plugins/. That should put a folder called pentaho-mongodb-plugin under plugins/, and if PDI is pointing at that plugins/ folder, it should load and use the plugin successfully at runtime.