Bad gas would not be covered by warranty. If it had water in the gas I doubt it would run at all. I would have them get a Yamaha tech to look at it.
If it sat for a long time the fuel line or bulb could have rotted and debris is clogging the filter inside.
I run mine at least twice a week, keep fresh gas at all times, and use the Ymaha fuel stabilizer and ring free.
The dealer having your boat is painful but once the issue is resolved it is a reliable motor.
2012 Skeeter ZX190
2012 Yamaha 175 HPDI