I've followed the way Jenkins generates update site and I've created our own update site based on our Maven repository. There's only few plugins listed in our update-center.json file. But when I add this update site to Jenkins with

hudson.model.Hudson.instance.updateCenter.sites.add(new UpdateSite("our_id", "http://our.site.com/update-center.json"));

the plugin manager lists all the available plugin updates twice. So if there's an update to plugin A from Jenkins update site, that's listed twice and same for plugin B update from our site.

I'm using Jenkins 1.428 but I've tried with more recent version 1.445 as well.