You can tell wp-Typography to not process the code inside certain elements — go to Settings ยป wp-Typography in your site’s backend and add the appropriate items to the appropriate areas. If you’re not sure what the appropriate items are, have a look at the source of one of the pages where you’ve got some LaTeX code added in. What tags are wrapped around your LaTeX code?
<math>...</math>— you should addmathto the HTML Elements box<div id="something">...</div>— addsomethingto the ID box<span class="something">...</span>— addsomethingto the Class box