I have this happen occasionally and my bike has less than 5k on it. I believe the reason this happens is due to the back slip clutch. Every once in a while if I get into a wierd shift pattern and let the clutch out and it spins up at the wrong time, it takes a second or two to engage properly. You can actually hear it kind of slapping around in there. I definitely do not think it is a problem, and you will find that as you get used to shifting this bike, it won't happen much if at all.
Another thing that happens that is similar is that you hit a false neutral and when you roll on and off the throttle it catches and goes into gear. That will take a second or two as well. It'll do this in 1-2, 2-3, and 3-4. Above that the space between gears is larger and it just stays in the false nuetral until you forcably shift it into gear.