There may be other unforeseen breakage primarily in the handbook portion of the wiki.
The Table Of Contents section of each "PC-BSD® Users Handbook" page may be the best workaround.
Talk:Installing Applications and Keeping PC-BSD® Updated
Another item to consider is installation of rpm files.
Some things that are designed as rpm may load as from ports and install in their proper location. However, other items (most notably flash) are an rpm file downloaded from a 3rd party site which requires an understanding of how to get it installed and/or where to drop it so it will get recognized.