I have a DPM 2012 server in my main Data center it is running as a VM on ESXi 5.1. I have a 2nd DPM 2012 server offsite at a hosted facility running the same way. DPM was in existence way before my time, it is set up to replicate all backed up data in site A to site B. Everything works fine except I can't figure out how to replicate to site B when I add new protection groups to site A.

My question is when new protection groups are added in site A how do I add the so they automatically go to site B? 

When I try to add a new protection group in site B I click on site A I get an error (DPM  is unable to enumerate contents in on the protected computer (ID: 38) ) and then it shows all the servers that where originally there under protected servers  but no newly added ones.

When it's working properly you should be able to go into DPM on site B and create (or edit) a protection group, find the site A DPM server in the list and expand that, then expand Protected Servers and drill down to the server and resource that you're trying to add. So you add them from the DPM server (site A), not directly from the protected computer.

Under the list there is a Refresh button (though in experience it doesn't always display as available) which you may need to click if the new object isn't displayed.