I have created several Schematron assertations and they are all running fine against my XML instances. However, I would like to structure the output of my error messages in
Actually to get a Schematron report as XML you should use SVRL. You can learn more about it here: Schematron Validation Report Language (SVRL)
The big advantage of using SVRL is that you can also get detailed information about where the assertion/report was triggered as an XPath.