I've filed it with Wikia, but I figured I'd let you all know about it too.
Our templates encompass the entire page to better control where everything sits in display.
This means that our references tag is placed within the page's template and no one has to write it in manually.
What I've noticed, is that on every Template I've converted to use PI in the infobox, the references tag within the same template does not display.
The only way I could make it work was by offering a field for the position it should go, and have the user enter the references tag there.
Examples:
The references tag should show in the footnotes section.