I will update the syntax documentation and mention the problem with the pipe symbol there, as well as mention that the \vert command should be used instead since they are equivalent.
This does not fix this problem in kramdown but in the LaTeX code which should be sufficient for all practical purposes.
Pull request #23 would probably fix this but in a backwards incompatible way. Since there are other situations like #135 where a pipe symbol also causes problems, a general solution would probably be quite complex.
the equation is as follows,
$P(X)=P\left(X | Y_1\right)$
the vercial bar will be converted to
<td>, which prevent mathjax to display it normally.
unless I write it as follows:
$P(X)=P\left(X \vert Y_1\right)$
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