Ok, so I may just be an idiot...
I seriously never heard a sound like this with my Ninja 250 or 650, so I'm still a bit skeptical that this is no big deal, but people who have seen/heard it in person don't seem to think it's anything to worry about.
You're lugging the engine. It would only be bad if you were riding around like that for a sustained period.
You're lugging the engine. It would only be bad if you were riding around like that for a sustained period.