Yes, Eclipse Marketplace unfortunately had a bug where they added in Juno to your updatesites just because you use the marketplace once (https://bugs.eclipse.org/bugs/show_bug.cgi?id=385334)
That results in you getting Juno when you do Help > Update from Eclipse.
They've fixed it now (it was a problem of the server side of eclipse marketplace) so if you start from Eclipse Indigo from scratch you should not see this problem of "behind-the-scenes Juno update".