Hello!

> Ref: NetBSD-1.3.1-i386 with current ports tree
--------------------------------------^^^^^

You mean pkgsrc, thus package tree? :-)

> I found some packages failed to built on my system as the
> destination path was hard coded to /usr/pkg in the patches files, although
> my prefix variable is set to /usr/local. 

How did you set that? I hope you set LOCALBASE in /etc/mk.conf.

> Do you consider this a bug needing reporting, if so who is the
> responsible person/group to notify.

Yes, if you set LOCALBASE in /etc/mk.conf to /usr/local and this got not
respected this is a bug. Please fill a bug report with send-pr(1) and
and set the category to pkg. But please douple check that you used an
uptodate pkgsrc :)

Greets
-- 

   Name  : Thorsten Frueauf            Milano@irc cri@onaliM       //
   E-Mail: s_frueau@ira.uka.de oder ukfy@rz.uni-karlsruhe.de     \X/