Code signing issue in Xcode version 8

I faced the same issue, fixed it without having to delete and download everything again.

I simply enabled Automatic Signing, waited for it to detect my signing certificates, and then disabled it. After that, I was able to reselect the desired provisioning profiles and the Signing Certificated were detected as they should.

I faced this too, and fixed it by:

1- removing all certificates of my account from keychain,

2- removing all provisioning profiles from xcode and then

3- downloading provisioning profiles again via xcode and also

4- adding certificates again to the keychain.

I was facing the same problem, I also tried removing all certificates from my login keychain, but the problem was still coming... Then, luckily one day, I opened system keychain and found that there were more than one distribution certificates added there.I deleted those from there. And then the problem got finally solved :)

So, if you are facing this problem, make sure you delete your certificates from login as well as system keychain and add them again to the login keychain. Hope it helps.