Are you hitting the water hard enough or going fast enough that you might be getting water into the air intake?
I’ve had mine under water to the handlebars I don’t have any issues just make sure everything is sealed up good Yamaha did good with the stock snorkeling I thinkHi everyone on my second Yamaha now my last one was a 350 grizzly brand new 10years ago an I went away from them cause I found with it use to splutter an cough when going through water just over the wheels, now 10 years later iv bought the new 700 kodiak an have the same issue in water? Am I the only unlucky one or is this common, many thanks