This is almost certainly down to the Mechatronics in the gearbox. It will come up as a temporary fault to start with. When you turn the engine off and restart it will disappear and you will have no warning lights on the dashboard. Sods law mine was just out of warranty. I bought the automatic as for some unearthly reason you cannot put a towbar on a manual 7 seat Kodiak because of the transmission and I have a bike rack. When you turn the ignition off and on and the warning disappears the car will work as normal for a god while. Sadly, it won't last long. Once you have the warning it's like the kiss of death to the gearbox. The only way you can find out for sure is by being put on a diagnostics machine four a couple of hours at £60.00 per hour. Once I read up on the fault I traded the car in. Its a real shame because it was a lovely vehicle with the panoramic roof but I bought the car for 20,400 and after a year of motoring it was going to cost around £2900 to fix.
If you are within the warranty period I would demand that they stick it on the diagnostics machine
To be honest, in this day and age, I am amazed that Skoda can get away with this without a product recall. The dealerships all know about it but choose to play dumb unless you push them.
I will get another Kodiak eventually but I will go for the manual gearbox next time and get a roof bike rack next time.