Dropping queries which have more than one result value (only one row, but more columns) can lead to uncertain data association.
Removing queries which are associated (per drag and drop) will eventually not remove all associated data. This is especially annoying if you want to generate an instance, which will fail if it encounters a token with a non-existing value.
Exporting data with the module <<Database to XML>> generates scrambled output (special chars). This can happen if the input data contains special characters. As a workaround, sometimes it helps to specify in the JDBC-Driver URL: "useUnicode=true" after the ? somewhere (read the docs of your driver). If this does not solve the case, the problem lies within the encoding handling of the JDOM. A newer JDOM version may help, because currently JDOM does not properly work with some encodings. Work in progress...
Validation of the output is not yet implemented, but at least you will be given hints while generating an instance that you don't forget to fill all required elements and attributes.