Moving Application to other folder I just upgraded from Snow Leopard to Mountain Lion. Now when I open my application folder via the Dock there are different programs present, e.g. Automator, which I moved to the "Utilities" sub-folder on Snow Leopard.

If I try to move them again to the sub-folder I get the message that the application cannot be moved to this sub-folder since the sub-folder cannot be changed.
You can still do something like sudo mv /Applications/DVD\ Player.app /Applications/Utilities/.

I ran into several issues after moving applications on 10.6. For example Console crashed on launch, even though that stopped happening on 10.7. And OS upgrades will add duplicate applications at the original locations as in your case.