I've tried searching for the answer to this problem but I don't quite know how to phrase it.
To describe the problem:
I have a document called New in a category General.
Within New, I create a link like this: <a href="[[~[[+id]]]]#anchor"></a>
However, the resultant link with friendly URLs turned on appears as sitename.com/general/general/new.html, with an extra appended "general" to it.
Is there something I'm doing wrong?
Never mind, I fixed it.
I added <base href="[[!++site_url]]" /> to the template and it works now!