Hi:
This is exactly what my 08 starting doing about 6000km on the odometer. Before that it seem very good and also never missed shifts and never went into false neutrals. It slowly started to make more clunking noises and finding false neutrals over the next 2000km. Did some digging on this site and found that there is a TSB from Suzuki warning that the Clutch spring bolts may back out with time and should be checked, locktite applied, and tighten to spec torque.
I also read about some mods that would help tighten the drivetrain and give smoother shifting. These were the Brock Ultra Clutch mod and the Factory Pro Evo Star shifter mods.
I ordered both kits, and did both mods together. When I took off my clutch cover on the right side all my clutch springs were loose! I could take them off with finger pressure only. So I am very glad I did this, as this could have caused more damage or created an unsafe condition while riding. I would highly recommend that you take your clutch cover off and check the tightness of the bolts to ensure they are not backing out. Here is the link to the TSB which clearly details what to do to correct the situation:
https://www.hayabusa.org/forum/gen-ii-busa-information/108236-service-bulletin-hayabusa-b-king.html
As for the mods listed above, you don't have to do them to correct this issue, but they do improve the shifting (Factory Pro EVO kit) making shifting more precise and less effort and the Brocks kit tightens up the clutch lever and makes the drivetrain "tighter".
Take care.
Rumble