> Using WinHTTrack I copied a site that has /%23us/ as
> part of the path. Online this doesn't cause a
> problem. However when browsing the mirror I can't
> navigate to any pages under this directory. Copied
> as #us.
Character hex23 is a # and that's a valid directory name character. But it's
not valid in urls as the # terminates the url and points to the anchor
portion.

Why can't you navigate there? 
Under show source what is the url /%23us/ or /#us/ (The latter would be a
httrack bug.)

Change the site local structure to anything other than site.