After installing MJ, a couple of my site's regular links wouldn't work. I would get the error "Incorrect usage of Mobile Joomla." Any ideas as to what that means.

www.mobilejoomla.com/documentation/12-getting-started/7-faq.html :

Incorrect usage of Mobile Joomla.

Most likely you assigned mobile template to a menu item. Note that mobile templates in MobileJoomla are not usual templates. They may be loaded through “Mobile Joomla Plugin” plugin only (and not as usual templates). That is why you cannot assign them to menu items or view them in preview mode. If you would like to give users a link to mobile version, do it with MobileJoomla’s MarkupChooser module.

Thanks, that was the issue.