Gathering route covers multiple zones
 

I did a route>current gathering locations in Stormheim. It created the goto routes for all herbs and ore. However it ended up guiding me out of Stormheim through to highmountain and other zones.

Can this be set to only one area? I have the gathermate addon for carbonite and imported all nodes.

Unfortunately, no, this problem can't be fixed. At least, not by Carbonite. It is caused by a flaw (if it can be called "a flaw") with WoW's mapping system. That particular problem has bugged Carbonite user's for an awfully long time (since Carbonite began, I think). :o

Does using the standalone gathermate fix it or any recommendations on a stand alone addon?

I am afraid I mis-spoke (mis-wrote?). This problem occurs because of the way that Carbonite's maps are built and there doesn't seem to be anything that can be done about it (or at least nothing has been found since Carbonite started). So, no, using the original Gathermate addon would not help. If you want to keep using Carbonite, you've just got to put up with it and continue on. Considering everything else that Carbonite does (and offer's), this is a small price to pay for using Carbonite. :o Besides which, any other map addon isn't going to have the ability to have Carbonite-like maps.