I am using fastlane to create and submit an application to testflight. Everything worked until I added Notification Content Extension and Notification Service Extension. Now apple pay and push notifications stopped working when building via fastlane.
**
My config file:**

lane :beta do
  api_key = get_api_key()

  build_no = ENV["CIRCLE_BUILD_NUM"]

  changelog = File.read("./release_notes.txt")

  prepare()

  provision = get_provisioning_profile(
    fail_on_name_taken: false,
    skip_install: false,
    api_key: api_key,
    filename: 'AppStore_' + ENV["BUNDLE_ID"] + '.mobileprovision',
    force: true
  )

  provision_name = lane_context[SharedValues::SIGH_NAME]

  update_code_signing_settings(profile_name: provision_name, use_automatic_signing: false)

  build_application()

  enable_automatic_code_signing(path: "./app.xcodeproj")

  upload_to_testflight(
    api_key: api_key,
    skip_waiting_for_build_processing: true,
    changelog: changelog
  )

  after_all do |lane|
    # This block is called, only if the executed lane was successful
    notification(message: "Release iOS beta finished")
  end

  error do |lane, exception|
    notification(message: "Release iOS beta error")
  end
end


lane :build_application do
    sync_code_signing(type: "appstore")  # see code signing guide for more information

    build_app(
        scheme: "app",
        export_method: "app-store",
        clean: true,
        configuration: "app",
        skip_codesigning: true,
        export_team_id: ENV["TEAM_ID"],
        export_xcargs: "-allowProvisioningUpdates",
        skip_package_ipa: false,
        # entitlements: "./app/app.entitlements",
        export_options: {
            provisioningProfiles: {
                 ENV["BUNDLE_ID"] + ".extension1" => "match AppStore " + ENV["BUNDLE_ID"] + ".extension1",
                 ENV["BUNDLE_ID"] + ".extension2" => "match AppStore " + ENV["BUNDLE_ID"] + ".extension2",
                 ENV["BUNDLE_ID"] => "match AppStore " + ENV["BUNDLE_ID"]
            },
        }
    )
end

lane :code_signing do
    update_code_signing_settings(
      use_automatic_signing: false,
      path: "./app.xcodeproj",
      targets: ["extension1"],
      team_id: "0000",
      profile_name: ENV["BUNDLE_ID"] + ".extension1"
    )
    update_code_signing_settings(
      use_automatic_signing: false,
      path: "./app.xcodeproj",
      targets: ["extension2"],
      team_id: "0000",
      profile_name: ENV["BUNDLE_ID"] + ".extension2"
    )
end

After adding two extensions (Notification Content Extension and Notification Service Extension), the standard build via Fastlane stopped working, because these two extensions need to be signed additionally.

After signing the extensions, the Fastlane build started working. But push and apple pay stopped working

As it turned out, the extensions were not signed. As a consequence, Apple Pay and Pushes don’t work (example of Pushes error: ITMS-90078: Missing Push Notification Entitlement – Your app appears to register with the Apple Push Notification service, but the app signature’s entitlements do not include the ‘aps-environment’ entitlement).

We generated the entitlement file using Fastlane, put it in the root of the iOS project directory, where the file should be. We tried to build the app through Fastlane. As a result, Apple Pay and Pushes did not subscribe.

We also tried to slip a link to the custom entitlement manually in Fastlane, but Apple Pay and Pushes didn’t fix it.