I have new iPhone 6s with mac running os x 10.11.13 and when i download updates of apps on phone they do not transfer to iTunes and to get them to be removed from updates i download them on iTunes what setting is wrong?

You are not doing anything wrong, this is a result of app thinning. This reduces the amount of space an app takes up on your phone by not installing the entire app, but only what is necessary for it to work on your phone. The app stored in iTunes on your computer can work on any compatible device, but the one on your phone may not.

Yes. You can only transfer apps from iTunes to iPhone, not the other way around.

New "App Thinning" with iOS9: To make apps smaller they are being customized for specific hardware when downloaded from Apple directly over-the-air to a device with iOS9. Apps downloaded directly to a device from Apple may no longer work on any other kind of device. Apple has decided there is no point in syncing these to a computer since each device should ideally get a customized version directly from Apple. If you want a backup copy on your computer you can transfer a non-thinned version directly from the Store to the computer which should you need it can be transferred to any i-device (but will take up more room). You may wish to enable automatic downloads on your computer so there will be a copy of all apps there as sometimes apps are removed from the Store: Turn on Automatic Downloads - https://support.apple.com/en-us/HT202180#computer Extra tips from sberman: Make sure "Apps" is checked. Also make sure the Apple ID shown just below "Automatic Downloads" is the same one you're using on the iPhone. - https://discussions.apple.com/thread/7488774?answerId=29896877022#29896877022

Here's the technical description: https://developer.apple.com/library/watchos/documentation/IDEs/Conceptual/AppDis tributionGuide/AppThinning/AppThinning.html - iOS9 App Thinning > "Slicing is the process of creating and delivering variants of the app bundle for different target devices. A variant contains only the executable architecture and resources that are needed for the target device." ... "The App Store will create and deliver different variants based on the devices your app supports."