I think this one is a bug in Xcode 5, as it didn't used to happen.  When I tried to validate an app it matched it to a different app (i.e. it had the wrong application name in the Organizer after I clicked validate.

I finally worked out that this was because I'd forgotten to click 'Ready to Submit Binary' in iTunes Connect

I've done this before and it's given me a sensible error message, so I guess this must just be a new bug.