Auto linker including tags inside hyperlinks

I have made a plugin that adds footnotes at the bottom of a page when you place something like this in a field:

{footnote}Source: http://www.domain.com{/footnote}

The problem I have is that EE automatically hyperlinks URLs and includes the tag {/footnote} inside the URL, so by the time my plugin gets the tagdata to replace footnotes the string looks like this:

{footnote}Source: <a href="http://www.domain.com{/footnote}">http://www.domain.com{/footnote}</a>

The workaround we’re using is to put a space after a URL like this:

{footnote}Source: http://www.domain.com {/footnote}

is there another solution? Can the plugin get the tagdata before these links are auto linked? Or is this a bug in EE that should be fixed?

PS: I found another bug with the auto linker that I reported here: https://support.ellislab.com/bugs/detail/15318/

Thanks.

Moved to Development and Programming by Moderator