There seems to be an issue with CocoaPods and XCode 10 where CocoaPods would force Always Embed Swift Standard Libraries to NO.

Until the issue is fixed, adding this to the bottom of your Podfile would force ALWAYS_EMBED_SWIFT_STANDARD_LIBRARIES to whatever you desire it to be:

post_install do |installer_representation|
    installer_representation.pods_project.targets.each do |target|
        target.build_configurations.each do |config|
            config.build_settings['ALWAYS_EMBED_SWIFT_STANDARD_LIBRARIES'] = 'YES'
        end
    end
end

Or for specific Pods only:

post_install do |installer_representation|
    installer_representation.pods_project.targets.each do |target|
        target.build_configurations.each do |config|
            if config.name == 'MyPOD' 
                config.build_settings['ALWAYS_EMBED_SWIFT_STANDARD_LIBRARIES'] = 'Yes'
            end
        end
    end
end