There is not enough information in your message to diagnose the problem. It looks like one possible issue could be that some CSS on your site is interfering with MathJax's CSS for displayed equations. You may need to use the developer tools in your browser to investigate that. Something may be changing the CSS setting for the "display" property for the elements generated by MathJax, for example, so that they are in-line rather than block. That seems the most likely source of the problem.
Without access to the site, or more details about the setup, it is hard to say.