The app store rules and review process are essentially the only thing that prevents Facebook from tracking you across all applications that use the Facebook SDK. It probably isn't possible to prevent tracking in a purely technical way. Even if two applications can't share data directly, they can each share fingerprinting information with a server, that allows Facebook to track you.

This sort of tracking can work even if you don't have a Facebook account, because so many different applications will include the Facebook SDK for ad tracking purposes.

Nothing specific to Facebook here, of course, it works the same way for any company with a large ad network.