Array and XML may be universal complex types, however, I would never trust that ColdFusion's proprietary interpretation of these types would work outside the CFML language. That is, if a ColdFusion function returns an array or XML, I would not presume it will be interpreted as such by a Java or PHP program, for example.
The most common, universal way of implementing XML webservices in ColdFusion is to use returntype="string". Another, not so common, way is to construct a SOAP response.
In any case, you should report your findings as a bug. If ColdFusion cannot handle the XML, it should return an error message, instead of an edited version of the XML.