xmlto relies on passivetex to convert the XSL-FO output from the DocBook XSL stylesheets to PDF. The error messages you cite are messages generated during the passivetex phase, not messages generated by any processing done with the DocBook XSL stylesheets.
You could file this bug against the passivetex package, but I doubt it will do you much good -- the developer of passivetex has not made any fixes or updates to it in many years. If you haven't given up on DocBook yet, you might want to try DBLaTeX instead. http://dblatex.sourceforge.net/ It works much better than passivetex and is still being actively maintained by a maintainer who responds quickly to bug reports. Anyway, bug 291813 should probably be closed out. Or at least filed against a different package. No fix for this can or will ever be made upstream in the DocBook XSL stylesheets. --Mike
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