@jhon258: OK. The most likely reason is malformed HTML passed to wp-Typography that gets “corrected” by the parser in a way that breaks the layout. To test if that’s the case, please remove the checkmark in the “Parser Errors” setting. If the layout looks normal, then that’s the issue and it should be fixed in the other plugin.
There might be something else going on here, without looking hte generated code (and what it should look like normally), I can’t really tell. However, wp-Typography is not changing any class names, certainly not in the way described in the initial post (those might be in the wrong place, but they are generated by another plugin).