RPi: SDL 2.0.3 to 2.0.4 - The key not recognized by SDL

My System:
Raspberry Pi 2 with Rasbian, Kernel 4.1.17
Gamepad: Wii U Pro Controller connected via Bluetooth
Keyboard: Small Bluetooth keyboard

I have RetroPie working on this system which is a compilation of several emulators for the Raspberry Pi. These emulators and their frontend make much use of SDL.

As long I had installed SDL 2.0.3 I had no problems.
After the installation of SDL 2.0.4 some days ago I get several of these error messages when I use Emulationsstation (a frontend for all emulators):

INFO: The key you just pressed is not recognized by SDL. To help get this fixed, please report this to the SDL mailing list sdl at libsdl.org EVDEV KeyCode 545
INFO: The key you just pressed is not recognized by SDL. To help get this fixed, please report this to the SDL mailing list sdl at libsdl.org EVDEV KeyCode 305

If I use sdl2 as driver in RetroArch (http://www.libretro.com/) my gamepad does not work properly anymore. My key bindings got messed up. Using udev instead my gamepad works again.
But those errormessages still remain. So I guess these messages are related to another problem which pop up when I use the frontend Emulationstation.

What can I do to solve this? If there is anything I can do to take a deeper look into this please let me know. But I must admit that I am no coder.