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Looks like your stylesheet is wrong. Probably you're outputting some text as the result of a select, but haven't output the actual tag the text belongs to. Without seeing the stylesheet, it's difficult to say
Yes, it's possible to use XSLT to generate something that isn't a well-formed XML document. For example you could have it output something with more than one root element. That isn't a problem if you output to a text file, but it would be a problem if you tried to output it to a DOM.
You aren't trying to write to an existing DOM, are you?