I've got an app that we've submitted dozends of versions to in the last 6 months and we do use APNS. I got the following email from Apple after upgrading to Xcode 8
We have discovered one or more issues with your recent delivery for APP_NAME. Your delivery was successful, but you may wish to correct the following issues in your next delivery:
Missing Push Notification Entitlement - Your app includes an API for Apple's Push Notification service, but the aps-environment entitlement is missing from the app's signature. To resolve this, make sure your App ID is enabled for push notification in the Provisioning Portal. Then, sign your app with a distribution provisioning profile that includes the aps-environment entitlement. This will create the correct signature, and you can resubmit your app. See "Provisioning and Development" in the Local and Push Notification Programming Guide for more information. If your app does not use the Apple Push Notification service, no action is required. You may remove the API from future submissions to stop this warning. If you use a third-party framework, you may need to contact the developer for information on removing the API.
After you’ve corrected the issues, you can use Xcode or Application Loader to upload a new binary to iTunes Connect.
The App Store team
What is weird is I went to developer.apple.com -> Certificates, Identifiers & Profiles and my AppId does have Push Notifications enabled still. I'm not doing anything different then I've ever done on it so am curious if the Xcode 8 update broke something. Any ideas?
BTW: The link they put for the Push Notification Programming Guide was broken in the email, so that's not a good sign.