They use road salt where you're at? Even well after the snowfall has gone, the road salt remains on the road for a while until rainstorms wash it away. If you've ridden it in late spring when the roads are wet, you'll still have some road salt on the bike to deal with. Gotta wash it right away to get that stuff off or it will start showing up as surface rust spots.

At least that's what it sounds like to me. You can try removing it with automotive cut and buff products to remove the surface rust, then keep the exhaust coated with a ceramic detail spray from now on so it doesn't return. Personally, I like M's Perfect-It 3 stage cutting products, been using that for detailing for many years, but its expensive for just a one-time use. I'd suggest finding an auto detail supply store near you and see if they have some Rupes D-A coarse and D-A fine, they come in small bottles and should be cheap enough to use by hand with a few microfiber towels. Finish it with a spray bottle of Technician's Choice TEC-582, another one that comes in small bottles.

 

I just polish mine after washing and it hasn't been a problem. As cheap as KTM is dont expect them to replace a component over surface rust.