When reporting the file contents of an iModel using imodelconsole, the report will include removed and deleted models, unless your query explicitly excludes these. But if an iModel is cloned, all previously deleted and removed files are copied through.
This means that the above imodelconsole report doesn't work as it doesn't see these files as being previously deleted.
It would be good when you clone an iModel to be able to clean up/compress the model to remove these deleted files.