I have also been receiving this error since last Friday:
ERROR ITMS-90034: "Missing or invalid signature. The bundle 'xxxxxxx' at bundle path 'Payload/xxxxxxxxx' is not signed using an Apple submission certificate."
I am building for iOS. I have built and rebuilt the certificates (CSR, Distribution, p12, provisional profiles) many times now and still not working. I am using Ionic to build the app. Everything works fine and is successful until I drop the IPA file into the Transporter app. As soon as it says it is uploading the app to the App Store, it throws the above error.
I have also tried the same process as above on one of my other apps and am receiving the same error. I did update the "Apple Worldwide Developer Relations Certificate Authority" certificate in Keychain. Everything says the certificate and private key are valid when creating.