I also updated Xcode 8 and ran into this. Both the Provisioning Profile and the Provisioning Profile (deprecated) were installed as empty in my project in Xcode 8.
I tried to return them to what was for each environment, but in the Debug environment all options in the drop-down list were deleted.
After creating the archive and downloading it to iTunes Connect, I received a notification that the provisioning profile was not entirely correct, which worked fine before Xcode 8.
After others sent a message saying that Xcode 8 received an update for their signature, I went to the general tab and noticed a new section that allows you to automatically control the Xcode signature. I checked this checkbox and now it looks like this:

I have not uploaded the new archive to iTunes Connect yet, but when I do, I will add an update here to see if it has enabled the Provisioning profile warning.
UPDATE:
After choosing Automatically manage your subscription in Xcode and resubmitting to the App Store, he still complains that it doesnโt work at all. You may need to delete and re-create all provisioning profiles for this to work. This is pain. Thanks Apple.
Joshua Pinter 09 Oct '16 at 18:42 on 2016-10-09 18:42
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