How is my theme incorrectly handling 404s? AIOSEO is clearly being informed that the page is a 404, as the rewritten title of the page is as specified in the 404 Title Format entry under the AIOSEO General Settings.
Thereafter AIOSEO is adding a Meta Description to the 404 page. I have turned off my CDN's optimisation process for you and provided a source extract from the 1st link I provided, so you can clearly see what AIOSEO is outputting -
<!-- All in One SEO Pack 2.0.2 by Michael Torbert of Semper Fi Web Design[739,841] -->
<link rel="author" href="https://plus.google.com/xxxxxxxxxxxxxxxxxxxxx/" />
<meta name="description" content="A study just published by the American College of Sports Medicine, shows that light exercise particularly just after meals may be able prevent high" />
var _gaq = _gaq || ;
ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
var s = document.getElementsByTagName('script'); s.parentNode.insertBefore(ga, s);
<!-- /all in one seo pack -->
As to what's hurting me, these URLs have been defunct for more than 6 months and I originally had a redirect coded directly into the htaccess file until I removed it in January. Only since upgrading AIOSEO from 2.0 has a single one of the URLs appeared on Google's 'HTML Improvements' list, and all of them are currently being listed directly under 'Duplicate Meta Descriptions'.