Well there are two types of "backwards", one is when you swap the black and red polarity when plugging into the Cortex, then the motor will run reverse from what you expect it to on the joystick controller. All you need do is rotate the pins in the port such that the red wire is closest to the middle of the Cortex.
The second is if you plug the wrong motor into a port. What happens here is that your joystick controller will operate the wrong side of the robot. All you need to do is swap ports.
In either case, plugging a motor into the wrong port or direction with a two wire motor will not adversely impact the Cortex.
I am assuming you are building the clawbot.