It seems like the strings in the markdown cells may need to be prefixed with r''
I can see the problem within a markdown cells:
$$ \begin{pmatrix} 1 & \frac{1}{2} \\ \frac{1}{2} & 1 \end{pmatrix} $$
$$ \begin{pmatrix} 1 & \frac{1}{2} \frac{1}{2} & 1 \end{pmatrix} $$
The first one shows up as 2x2 while the second shows up as 1x4 most likely because '' is interpreted as '' unless the string is prefixed by 'r'
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