This has been corrected, but is not yet available in a public release, it will be in 4.0.3, see
http://git.gnome.org/cgit/libgda/commit/?id=26f214fbfbd99ded4b30576999285c1fb7eba06f for details. The problem is due to the fact that Libgda adds some extra columns to SELECT statements in SQLite to be able to generate update, insert and delete statement when modifying the results of a SELECT and there was a bug in the process.
In the meanwhile, you can use Libgda from git or I can send you a tarball with the current sources which will become version 4.0.3.
Regards,
Vivien