Chris, it might help if you could include a photo of the two pin plug. However if you think you might have reversed the plug when plugging it in, then try unplugging and reversing the plug to see if that cures the problem. Many 12v plugs have different size pins such that they can only be plugged in one way round which would make it impossible to inadvertently connect it the wrong way around. If the plug can be connected incorrectly then try the system, you can do this without moving the boat away from your berth. I’m guessing that the autopilot system you have is essentially a wheel pilot rather than a below deck system, but once connected and switched on you can press one of the course adjustment buttons, and see which way the wheel turns. If it goes the wrong way, then the polarity of the way the plug has been connected could well be at fault. If it keeps going the wrong way despite how the plug is connected, then we need to check further for some other fault.
Let us know how you get on with reversing the plug, good luck.