Normally the TeX filter filter and MathJax are compatible. If the Moodle Mobile App is enabled, running both is recommended because MathJax is not yet supported in the app.
HTMLTidy is the likely culprit (see MDL-47533). The system admin may have installed the PHP Tidy extension on a server where it was missing. The filter does nothing unless the extension is enabled.
This filter frequently causes problems with cloze questions. As far as I know, it no longer provides any useful service. It would be nice to remove it to reduce confusion.