Resigning for App Store distribution not working, get three errors when uploading

[andersemil]

ERROR ITMS-90035: “Invalid Signature. The binary with bundle identifier ‘...’ at path [....app] contains an invalid signature. Make sure you have signed your application with a distribution certificate, not an ad hoc certificate or a development certificate. Verify that the code signing settings in Xcode are correct at the target level (which override any values at the project level). If you are certain your code signing settings are correct, choose “Clean All” in Xcode, delete the “build” directory in the Finder, and rebuild your release target.”
ERROR ITMS-90046: “Invalid Code Signing Entitlements. Your application bundle’s signature contains code signing entitlements that are not supported on iOS. Specifically, value ‘*’ for key ‘com.apple.developer.associated-domains’ in ‘Payload/....app/...’ is not supported.”
ERROR ITMS-90179: “Invalid Code Signing. The executable ‘Payload/....app/...’ must be signed with the certificate that is contained in the provisioning profile.”

[andersemil]

Using Xcode 10.3 on macOS Mojave 10.14.6

[andersemil]

Extracting the original entitlements from the app and adding the --deep flag to codesign arguments seems to fix these problems