I have the same problem with the PS3 controller. The games wont load if it is connected either via bluetooth or usb. When I disconnect the games load. However in game I am not able to anything as I have apparently not been able to configure any controls for the emulator.
I would much appreciate if anyone can point me in the right direction to where I might learn more about the controls for this emulator and how to configure.

Using RPI2 and version 2.6.0 of retropie