I am not clear yet exactly what your configuration is. Normally neither TeX notation filter nor MathJax filter use single $ as a delimiter. The default configuration uses either double $ or \( to delimit TeX code from regular text. MathJax can be configured to use a single $, but that would require changing the configuration options. That may be where the problem is. Can you give us your configuration? You may also try using the standard delimiters.
Mathematics tools
latex equation
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