I'm amused by the fact that a link is broken in the very first paragraph due (presumably) to a poor linkifier and what it thinks of URL encoding (or potentially other syntactic features of the source language). The document was probably done in Markdown, and the trailing right parenthesis in the link is not treated as part of the URL, so instead of being http://en.wikipedia.org/wiki/Java_(programming_language) the link target becomes http://en.wikipedia.org/wiki/Java_(programming_language with the parenthesis appearing after the link.
I think you're really close, except I think that they have an autolink regex to find unanchored URLs and anchor them. And that it is that regex that is failing to deal with Wikipedia's brackets in URLs.
Assuming Markdown, that would be::
Bad parser.