Thanks for bringing this to the attention of the community and apologies for the issues you’ve been having. This issue stems from having a copy of the expired WWDR Intermediate certificate in both your System and Login keychains. To resolve the issue, you should first download and install the new WWDR intermediate certificate (by double-clicking on the file). Next, in the Keychain Access application, select the System keychain. Make sure to select “Show Expired Certificates” in the View menu and then delete the expired version of the Apple Worldwide Developer Relations Certificate Authority Intermediate certificate (expired on February 14, 2016). Your certificates should now appear as valid in Keychain Access and be available to Xcode for submissions to the App Store.
As noted in a comment below, the expired certificate also needs to be removed from the
login section, as well:
To all that cannot get it working despite the instructions... There are two expired WWDR certs. One is in login keychain, and the other one is in the System. You have to delete both of them in order to make things working