I assume it is a 4 stroke and you are getting water in your oil?
Crankcase venting could be an issue directly related to running temperature. If the motor is not reaching normal opp temp, it will not evaporate condensation from within the sump (oil pan). Try an infra-red temp gun to see if both sides of the engine are reaching about 150. Start by replacing your thermostats . Could also be a leaking gasket somewhere.- cylinder head or powerhead gasket. Check with a Yamaha dealer as they would have service bulletins, Yamaha factory tech assistance, and prior experience with this issue. Unattended water in your crancase oil will lead to rod bearing failure. I recently had a 50 hp 4 stroke that failed from water in the crankcase. Someone removed the thermostat causing it to run cold leading to water build-up.
Try this for now- Store your motor trimmed down after use. After a few days sitting, you can pull the drain plug and let the water out as it will have settled to the bottom of the pan. Top off level with fresh 10W30 Yamaha oil. This way you will also know how much water is getting in. A 2016 should still be under warranty !