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?

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It appears that the problem is caused by a combination of xltxtra redefining \textsuperscript and the font not containing true superiors for all numbers. The xltxtra package is loaded from one of the pandoc templates and superscripts appear as expected when it's removed. There are more details in answers to some similar questions here and here.

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