I've had this same issue recently, there is now a default workflow for xcode cloud that performs the post clone step that was provided by @BEK ROZ
I also had the same issue locally when building a VueJS app with Ionic/Capacitor
Before now my knowledge of iOS builds is precisely zero, so excuse innocence, but I found the issues were relating to the *xcconfig files. Every capacitor module that you install with npm will have it's own xcconfig file for debug and release - Stored in:
ios/App/Pods/Target Support Files/{{ Module Name }}/{{ Module Name }}.debug.xcconfig
ios/App/Pods/Target Support Files/{{ Module Name }}/{{ Module Name }}.release.xcconfig
I've only installed two plugins, so I uninstalled one of them, which was cordova-plugin-screen-orientation, synced and then archived (steps below) and this time it passed.
# Remove a capacitor module with npm e.g. cordova-plugin-screen-orientation
npm uninstall cordova-plugin-screen-orientation
# Sync the iOS plugins to remove the plugin from your Podfile (ios/App/Podfile)
npx cap sync ios
So I'd recommend going through all of the plugins you've installed and see if any of them are playing up. Then go back to xcode, run "Product -> Archive" from the menus to start a new build or push your changes and let xcode cloud do the heavy lifting for you.
Good luck