Our colleague has already created an issue in the SQLite JDBC tracker https://github.com/xerial/sqlite-jdbc/issues/547. It's possible that the problem is with JDBC or with our own code. But the reason to write about it here is that the strange file is a native SQLite temporary file in the SQLite temp directory. As far as I know, neither the JDBC driver nor our code manages these files at all. All that we do is set the temp_store_directory pragma when the connection is established.