Posting this answer because it is a bit of a strange issue.
When the patch top is created, it connect to the database via the service ebs_patch. On the database tier the listener you refer to in you init file as LOCAL_LISTENER needs to have the service ebs_patch registered to it. So for example:
my listener is E1HUB02. When I did a status on E1HUB02 , the service ebs_patch was not registered. Since this is supposed to happen dynamically, if its not registered you will get the AC-50480: Internal error occurred: java.lang.Exception: Error while generating listener.ora. Because you are unable to connect to the ebs_patch service. My problem specifically was that my E1HUB02 listener was down when i configured my database. But a listener named 'LISTENER' was running on port 1521. Also I had unset LOCAL_LISTENER when i did my clone so, when i brought up the database it automatically registered ebs_patch with the listener on port 1521. I didn't realize this, and brought up my E1HUB02 listener on port 1528. My database registered with 1528, but the ebs_patch stayed on 1521 listener. Once i fixed all of this mess, everything worked perfectly.