The simple way to troubleshoot is to substitute another (working) remote controller and see if both colors work.
The yellow wire from the track switch is either +5VDC or -5VDC with-respect-to-ground (the black wire) and there are diodes in front of the green and red LEDs in the controller such that + lights one pair of LEDs and - lights the other color LEDs. Thus, either the diode in front of the red LED has failed or the board in the track switch has failed.