One of the issues with TrackBack currently is that the RDF that TrackBack inserts into pages breaks XHTML validation. Now, whether you should care about this or not is up to you--the fact is, the RDF is valid, and if the rest of your document is valid, then really, you've met the goal of validation, if not the present reality.
But the fact remains that we do want to fix this issue and we'd like to hear your thoughts on the matter. We are planning on adding xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns" to the <html> tag in the default templates for the next release; while the W3C validator still declares the document invalid, this seems to be the right thing to do. We do want W3C validation, though, so if you have ideas, let us know. Phil Ringnalda has posted a great explanation of the issue with links to further resources and (perhaps) a start to one of the possible solutions.