问题已解决，分析了下看了下系统的证书管理，发现钥匙串中证书助理模块在系统更新 10.12 的时候没更新完善，但是系统没有报错，重新更新了最新系统，重新导入开发证书，App 编译需要的各种证书，报错解决！

很奇怪为什么 Xcode 里面没有出现编译错误，但是命令行编译不行，所以看来两者还是有区别的。

DesiredCapabilities capabilities = new DesiredCapabilities();
    // capabilities.setCapability("maxTypingFrequency", 45);
    capabilities.setCapability("useNewWDA", true);
    capabilities.setCapability("newCommandTimeout", "60000");
    capabilities.setCapability("wdaConnectionTimeout", 60000);
    capabilities.setCapability("automationName", "XCUITest");
    capabilities.setCapability("BROWSER_NAME", "");
    capabilities.setCapability("PLATFORM", "Mac");
    capabilities.setCapability("deviceName", ios_deviceName);
    capabilities.setCapability("platformName", "iOS");
    capabilities.setCapability("platformVersion", ios_paltformVersion);
    capabilities.setCapability("bundleId", "com.everbridge.mobile.iv.Recipient");
    capabilities.setCapability("udid", ios_deviceid);
    capabilities.setCapability("xcodeOrgId", "XXXXX");
    capabilities.setCapability("xcodeSigningId", "iPhone Developer");
    capabilities.setCapability("showXcodeLog", "true");
    capabilities.setCapability("clearSystemFiles", "true");

Appium Log:

[Appium] Creating new XCUITestDriver (v2.36.0) session
[Appium] Capabilities:
[Appium]   clearSystemFiles: 'true'
[Appium]   xcodeOrgId: '4H3LPY68H3'
[Appium]   bundleId: 'com.everbridge.mobile.iv.Recipient'
[Appium]   deviceName: 'iphone 6S'
[Appium]   xcodeSigningId: 'iPhone Developer'
[Appium]   PLATFORM: 'Mac'
[Appium]   showXcodeLog: 'true'
[Appium]   newCommandTimeout: '60000'
[Appium]   BROWSER_NAME: ''
[Appium]   platformVersion: '10.3'
[Appium]   useNewWDA: true
[Appium]   automationName: 'XCUITest'
[Appium]   platformName: 'iOS'
[Appium]   udid: '6b41dfda68535e5614c40e807b25442645d5c729'
[Appium]   wdaConnectionTimeout: 60000
[Appium]   noReset: true
[debug] [XCUITest] XCUITestDriver version: 2.36.0
[BaseDriver] Capability 'showXcodeLog' changed from string to boolean. This may cause unexpected behavior
[BaseDriver] Capability 'clearSystemFiles' changed from string to boolean. This may cause unexpected behavior
[BaseDriver] Capability 'newCommandTimeout' changed from string ('60000') to integer (60000). This may cause unexpected behavior
[BaseDriver] The following capabilities were provided, but are not recognized by appium: PLATFORM, BROWSER_NAME.
[BaseDriver] Session created with session id: 534e8017-32d9-4534-bf2d-ea5f0769f298
[debug] [XCUITest] Xcode version set to '8.3.3' 
[debug] [XCUITest] iOS SDK Version set to '10.3'
[debug] [BaseDriver] Event 'xcodeDetailsRetrieved' logged at 1498805815777 (14:56:55 GMT+0800 (CST))
[debug] [XCUITest] Available devices: 6b41dfda68535e5614c40e807b25442645d5c729
[debug] [XCUITest] Creating iDevice object with udid '6b41dfda68535e5614c40e807b25442645d5c729'
[XCUITest] Determining device to run tests on: udid: '6b41dfda68535e5614c40e807b25442645d5c729', real device: true
[debug] [BaseDriver] Event 'appConfigured' logged at 1498805815877 (14:56:55 GMT+0800 (CST))
[debug] [BaseDriver] Event 'resetStarted' logged at 1498805815878 (14:56:55 GMT+0800 (CST))
[debug] [XCUITest] Reset: fullReset not set. Leaving as is
[debug] [BaseDriver] Event 'resetComplete' logged at 1498805815878 (14:56:55 GMT+0800 (CST))
[debug] [iOSLog] Attempting iOS device log capture via libimobiledevice idevicesyslog
[debug] [iOSLog] Starting iOS device log capture with: 'idevicesyslog'
[debug] [BaseDriver] Event 'logCaptureStarted' logged at 1498805816361 (14:56:56 GMT+0800 (CST))
[XCUITest] Setting up real device
[XCUITest] Using WDA path: '/usr/local/lib/node_modules/appium/node_modules/.2.36.0@appium-xcuitest-driver/WebDriverAgent'
[XCUITest] Using WDA agent: '/usr/local/lib/node_modules/appium/node_modules/.2.36.0@appium-xcuitest-driver/WebDriverAgent/WebDriverAgent.xcodeproj'
[debug] [XCUITest] Capability 'useNewWDA' set to true, so uninstalling WDA before proceeding
[XCUITest] Shutting down sub-processes
[debug] [XCUITest] Removing WDA application from device
[debug] [BaseDriver] Event 'wdaUninstalled' logged at 1498805816766 (14:56:56 GMT+0800 (CST))
[debug] [BaseDriver] Event 'wdaStartAttempted' logged at 1498805816767 (14:56:56 GMT+0800 (CST))
[XCUITest] Launching WebDriverAgent on the device
[debug] [XCUITest] Carthage found: '/usr/local/bin/carthage'
[debug] [XCUITest] Killing hanging processes
[debug] [XCUITest] Starting iproxy to forward traffic from local port 8100 to device port 8100 over USB
[debug] [XCUITest] iproxy exited with code '208'
[debug] [BaseDriver] Event 'wdaStartFailed' logged at 1498805816959 (14:56:56 GMT+0800 (CST))
[debug] [XCUITest] Unable to launch WebDriverAgent because of xcodebuild failure: "iproxy exited with code '208'". Make sure you follow the tutorial at https://github.com/appium/appium-xcuitest-driver/blob/master/docs/real-device-config.md. Try to remove the WebDriverAgentRunner application from the device if it is installed and reboot the device.

模拟器运行没问题，真机有问题，查了很多说是签名问题，可是已经设置了签名，为什么还会报这个错误？？？求助！！！