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This kind of thing just happens with some pdf documents. I think it's a side effect of pdftohtml, which is the engine that Calibre uses to convert pdfs. The new pdf engine may fix some of these cases, but it's not ready yet.
You'll need to use Sigil or a text editor to do a find and replace after conversion. There isn't any feature in Calibre at this point that lets you do search and replace on screwed up quotes.
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