I received the following email from Apple when I submit an app update:
We have discovered one or more issues with your recent delivery for \"Project
1) Go to project settings, choose PROJECT (above targets), go to Build Settings
2) Press Add User-Defined Setting and add APP_BUILD and APP_VERSION
3) In your targets go to Info and replace Bundle version to $(APP_BUILD) and Bundle version string to $(APP_VERSION) in all targets and extensions where you need to sync.
4) Woila! You should change bundle versions only in one place - in Build Settings of your PROJECT.