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This cset: https://dvcs.w3.org/hg/csswg/rev/6142#l1.163 introduced an additional stray <head> and <body> tag into the middle of the flexbox spec. (neither of which are ever closed) I suspect both of those tags want to be removed. (Neither of those tags seem to exist in the Overview.src.html files, so this might indicate be a bug in the .src.html --> .html processor...)
Looks like a bug in the spec processor - it seems to break when it sees the <style scoped>. It doesn't appear to have a visible effect on the spec, so I'll just ignore it for now and manually remove it when we publish for CR.
Actually, fantasai fixed it by moving all the styling up into the head. I call that "coddling the preprocessor". It has to grow up sometime!