Pullquote appears over the header

My first suggestion would be to switch to the default theme and see if it still happens. If it doesn’t happen with the default theme, then it’s a bug in your theme.

A common cause of pull-quotes occurring twice is buggy themes that call the wp-head stuff twice. It should only be called once.

As for appearing over the header, this could be a nesting issue, again with the theme. Make sure the <span> is located inside a paragraph and see if that fixes it. In terms of HTML, the pull-quotes appear at the top of the Parent of the <span>. Thus if the span is inside a paragraph, the quote should be at the top of the paragraph.