Only issue I've run into so far is that cross-references to theorem numbers don't seem to always work correctly, e.g. you'll see a lot of "Theorem ?" in https://www.arxiv-vanity.com/papers/1607.06711/.
That said, on cursory look, this is pretty impressive. latex->web converters have existed for a long time, and this appears to have navigated some aspects quite well!
Only issue I've run into so far is that cross-references to theorem numbers don't seem to always work correctly, e.g. you'll see a lot of "Theorem ?" in https://www.arxiv-vanity.com/papers/1607.06711/.