I discovered a persistent little bug: If the last line of a Markdown file is a hyperlink, Hugo will render it as plain text. For example, this Markdown code:
[1]: http://www.website.com
… gets rendered literally as "[1]: http://www.website.com"
on the final page—the actual hyperlink is not inserted at the correct place referenced earlier in the .md file.
The current workaround is to add a carriage return to the end of the .md file so that the last line is blank.
Hopefully this little bug can be fixed in the next release.