An app downloaded from Appstore earlier would have all the files related to that app irrespective of whether your present device supported the feature or not.
App thinning is a feature that would only allow the software that is compatible with the specific iPhone to be downloaded. This would mean if your model is not supporting Apple pay, then the app that you downloaded will not contain files that would support the same.
iOS 9.0.2 update
Apple was supposedly introduce this feature in iOS9, but due to some bugs in iCloud the introduction was delayed. Now, 9.0.2 update has come up with app thinning feature so that the old iPhone model users have to think less about frequent out of space warnings.
Even after updating you are finding the error messages, then try this 3 things for overcoming the problem.