Do you mean the gear selects with a clunk and a jerk, is it worse first thing in a morning say?
If so this is common to a lot of bikes, one thing that helps is to give the throttle a few blips whilst simultaneously pulling in the clutch-lever and releasing again. Also make sure your tickover is set to spec, around 1100 rpm, high tickover will make selection very clunky.
If it stays bad you might need your clutch adjusting to spec or even the plates and basket checking.
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