Yeah, that's a common error among Markdown writers. It's too easy to forget the last bracket, especially if you are putting a link inside a parenthetical comment in the first place.

Fortunately, it's easy to detect programmatically. I have a little shell script which flags problems in my Markdown files: http://gwern.net/markdown-lint.sh

In this case, you can use Pandoc | elinks -dump to get a rendered text version, and then simply grep in the plain text for various things like "-e '(http' -e ')http' -e '[http' -e ']http'"