To recreate, do this:
import maec
obj = maec.parse_xml_instance("maec_4.1_examples/package_manual_analysis_example.xml")["api"]
print maec.package.package.Package.from_dict(obj.to_dict()).to_xml().encode('utf8')
(the final encode() is because I'm printing to an ASCII terminal; it isn't going to affect the problem).
In the output, search for BAD_XSI_TYPE, which occurs all over the place.