Thanks for reporting this. It looks like the MathJax embedding they use produces two blocks that look the same to me. The second one has a class attribute ‘MJX_Assistive_MathML’ and is hidden with CSS using a combination of height: 1px and position:absolute. So your browser effectively hides it from you, but Push to Kindle sees two blocks that should be rendered.
In such cases we usually apply custom rules to remove the second instances that cause this kind of duplication in the final result. I’ll try and do that for github.io articles. Will update again here when that’s done.