In the example below, the numbers 1-3 are in superscript as footnote markers while 4-9 and 0 are not. This occurs when the main font is Quattrocento Sans (using \setmainfont{Quattrocento Sans}) but not if there is no \setmainfont declaration.
There is no extra configuration of the footnotes which are produced from urls with \renewcommand{\href}[2]{#2\footnote{. #2 \url{#1}}}
What is going on? is it font problem (since i get the same results on OSX and Debian)? xetex? something else?

xltxtrasomehow? http://tex.stackexchange.com/a/80028/5049 – cgnieder Jun 17 '15 at 13:51