You mean like the third paragraph in this edit?
That's kind of a tricky case. The problem is that the change is in the middle of an equation, so the diff engine sticks some extra markup in there to highlight it, causing MathJax not to recognize it as a valid equation at all. To fix it, either:
a) the SE diff generator would need be changed to treat MathJax sections as atomic blocks (which would have the unfortunate side effect of always showing the entire equation as changed, even if the actual change was to a tiny part of it), or
b) MathJax itself would have to be somehow tweaked to recognize the diff markup and replicate it in the rendered equation. I've done a bit of MathJax hacking myself, but that sounds way beyond my skills.
I suspect the first option above would be the more practical one, but I can't really tell — AFAIK, the diff generation is done on the server side, so only SE developers actually know how the code works.