The MindCuber program uses a special ColorSensorRGB block (see section 2.1 on the MindCuber EV3 Page). This block uses a "hidden" mode of the LEGO EV3 Color sensor to read raw RGB values. This mode is not available in the Commander app for Android or iPhone.
The mode you are seeing in the Command app (with only the red LED) is the reflected light mode.
If you want to see what the MindCuber program sees, then you will need to write a program using the LEGO MINDSTORMS EV3 desktop software along with the special ColorSensorRGB block from the MindCuber web page.
The MindCuber program does not actually care what color each square on the Rubik's cube is. It actually guesses which squares are white and then sorts the remaining colors by hue. So, observing the RGB values directly will probably not provide much insight. You will need to study the MindCuber program and copy parts of it to debug what the MindCuber program is "seeing".
There is also a list of troubleshooting tips on the MindCuber EV3 Page as well as a link to the MindCuber Facebook page which is the official way to get support for the MindCuber.