I was having the same issue on mine. It was my shifter the bar that the shift linkage hooks up to that turns the star gear. One of the bad had snapped off.
^ +1First and most common place to look........
the shifter pivot off the footpeg bracket, I see these things rusty and all grimed up often and it will restrict movement and if bad enough hold the shift pedal from returning
Sadly it is held in with a bolt from the back of the footpeg bracket on most models and it is red loctited in, so heat and good tools would be your friend!
You'll notice that when you start to push the bike more and more .. you're shifts will become a lot smoother .. if you're switching gears at lower rpms the shits won't be so smooth .Well this is odd. I just bought a 14' 636 and I am having the same issues. Sometimes the shift is smooth and easy, other times it goes in gear but feels "jagged" or rather not smooth. I only have 126 miles on it, and I have not been hard on the bike. I am starting to get a little worried because my 300 never had this issue. I notice there is play in the clutch lever but not more than normal. Any guesses?