Those problems are normally Pandoc parsing errors. Considering it's open source, perhaps we should print the error message so people can actually help fix it...

The MathJax failures are either things that MathJax doesn't support, or use of \DeclareMathOperator which we haven't added support for yet.

Edit: Added a more useful error message. :) https://www.arxiv-vanity.com/papers/1608.04012/