Previously with Xcode 7.3.1 I was able to build directly over my app store app on my iPad and test the upgrade scenario, which worked perfectly fine. This week I upgraded to
To fix this just enable "Automatic manage signing" from general tab of project settings.
I had also problem for running app on my device directly from xcode 8. Deleting and generation profile and certificate did not worked for me. But enabling "Automatic manage signing" worked for me.
Hope this helps!
Check this question of mine: Xcode 8 shows error that provisioning profile doesn't include signing certificate