Been fiddling around with the blog and realized that octopress has a limitation as of the last stable version; it’s designed to work by default with rdiscount, which is a markdown parser. Quite a few people using markdown use extensions from markdown extra which allows for prettily formatted footnotes. Rdiscount does not support any of those extensions, and while octopress can be told to use 2 other markdown parsers1, the default theming isn’t setup to format footnotes nicely.
Addendum: I spent some more time googling and discovered a few sites with some helpful code snippets and suggestions. So for now I’m using kramdown and have functional footnotes.