An example that comes to mind that I've seen is an anonymous app that allows for blocking users; you can programmatically block users, query all posts, and diff the sets to identify stable identities. However, the ability to block users is desired by the app developers; they just may not have intended this behavior, but there's no immediate solution to this. This is different than 'user_id' simply being returned in the API for no reason, which is a vulnerability. Then there's maybe a case of the user_id being returned in the API for some reason that MIGHT be important too, but that could be implemented another way more sensibly; this leans more towards vulnerability.
Ultimately most fingerprinting technologies use features that are intended behavior; Canvas/font rendering is useful for some web features (and the web target means you have to support a LOT of use cases), IP address/cookies/useragent obviously are useful, etc (though there's some case to be made about Google's pushing for these features as an advertising company!).