I'm struggling to understand the question. An app designed for one OS isn't guaranteed to work on another OS. iOS5 apps don't work on the latest Android OS, for example, and they don't work on Windows. That's because they are different OS's.
iOS6 is not the same OS as iOS5. It's not so different from iOS5 as the latest Android OS, but it's still different; otherwise it wouldn't be a new OS.
So your question should really be "I have a new OS and yet some of my apps still work? How is that possible?" rather than the other way round. And the answer to that question is that iOS6 is different from iOS5, but not so different that every aspect is changed; and if an app doesn't use any of the aspects that were changed, it will contibue to work.
This is exactly why we have beta periods for iOS versions. It's not to find bugs; it's to allow developers (the only people with legal access to these versions) time and opportunity to rewrite their apps to work with the new OS if necessary.