Math.SE moved to the beta version of MathJax v2.1 on Monday. Did you upgrade to iOS6 around then? It turns out that there was a line-breaking problem in MathJax v2.1 (see this post), and the lines that are giving you the processing errors are the ones that would need to be wrapped for your device, so I suspect it is that problem. A bug fix was made available yesterday morning around 9:00AM Eastern time, but you might need to clear your cache and/or restart the browser in order to get the updated version.
In iOS you can clear the cache through the system preferences app, in the Safari preferences (I don't remember exactly where). You can restart the browser by double-clicking the home button on the device: you will get a line of all the running application at the bottom of the screen; click and hold one of them to start them jiggling, then click the minus sign at the upper left of the Safari app to stop it.
If you still experience problems after clearing the cache and restarting the browser, let me know.