Water pump gasket/seal would most likely put coolant in the crankcase / gearbox oil since the cooling system is under pressure and the gearbox isn't. That is ofcourse unless the KTMs are doing things different. The water pump is usually driven off something in the crankcase / gear box.
Not being familiar with how KTMs do things I'm basing my guess off other 2 stroke engines. My first inclination might be Head gasket since the cylinder compression could push cylinder mixture into the cooling system.