Steps:
1. Build and Run user's project ("GameCntrollerSample.zip") on iOS device
2. Connect a game controller
3. Press buttons on game controller

Expected behavior: KeyCode is shown in the screen
Actual behavior: Text on the screen stays the same, Input.GetKey() does not register that buttons were pressed.

Test results:
iPhone SE | iOS9.3 | reproduced
iPhone 6 | iOS8.0 | not reproduced
iPad 5th gen | iOS10.3.3 | not reproduced
iPod 6th gen | iOS10.2.1 | not reproduced
iPhone 7 plus| iOS10.3.2 | not reproduced

Reproduced with: 2017.3.0a3, 20172.0b11, 2017.1.1p2, 5.4.6f1.

Used Horipad Ultimate game controller.

BY DESIGN:
This happens because 'GameController.framework' is not included in the Xcode project. We add it automatically if 'UnityEngine.Input.GetJoystickNames()' is called anywhere inside the Unity project to avoid including it in projects which do not use gamepads. So simple checking if any controllers are connected with 'Input.GetJoystickNames()' before executing any gamepad related code should fix this issue. Alternatively, you could add 'GameController.framework' to your project either manually or using https://docs.unity3d.com/ScriptReference/iOS.Xcode.PBXProject.AddFrameworkToProject.html.