There is a discrepancy between how the UpIntfName DB variable handles sub-interfaces and how routers/switches handle them. UpIntfName selects interfaces that don't have 'shutdown' in their config. For example:
description physical interface
With the above configuration a 'sh int desc' on the router will show the sub-interface as being 'admin down' because it's parent physical interface is shutdown. However, UpIntfName will include the sub-interface in any templates you deploy. To correctly exclude the sub-interfaces from UpIntfName you have to enter the shutdown command on each of them (and probably re-sync the device in Prime). Was getting confused as the show commands on the router said the subs were shut and it was only when looked at 'show run int' noticed they're actually not.