Yes, but not that quick, if you were using the gas from the Marina in PC, it's Ethanol free.
I've had good luck using Sta-Bil for years, get the green "Marine" kind, or if you use the red, mix at twice strength, it won't hurt.
An inline
fuel filter would most likely have caught the
water first too.
I'd be astonished if it were really "ruined", I'd bet a good
cleaning is all it needs, maybe replace the jet of something if it is "ruined", but 2 months is too short a time to be ruined, I think.
Maybe try a different Yamaha dealer, but if it is damage from water in
fuel, I'd be surprised if that is covered under warranty.