As you haven't said "No, it's not that", I will expand a bit.
Remember that the clutch and gearbox are the same as on the manually controlled bikes. The clutch is operated by a motor that disengages it when you change gear, then re-engages it in the new gear. But it doesn't just drop in the clutch any more than would a rider while holding the throttle at high engine revs (unless he wanted to attempt a wheelie or make the rear tyre skip!).
On a bike with conventional controls, when you change up you would momentarily dip the throttle as you pull the clutch, change gear, then open the throttle as you re-engage the clutch, this allows the engine revs to match the new gear road speed. With your Gen 2 YCC-S, the bike has no direct control on the throttle, so if you don't allow the engine to match the new gear road speed, the MCU will hold the clutch slipping. This allows some torque through the clutch, meanwhile doing its best to reduce engine power by retarding the ignition. Crude, but it's all the control over the engine power it has. Makes for a very tardy gear-change (and not very kind to the clutch plates), but it does protect the rider from the rear tyre losing grip if he changes gear without proper throttle control in a slippery corner.
When you change up, learn to momentarily dip the throttle as you flip the switch (I never use the foot change, just my fore-finger to change up or down), or blip the throttle open a bit as you change down, just as you would for a smooth change on a conventional bike. Remember, you are always trying to reduce the torque in the gearbox whilst changing gear.
The throttle dip or blip is only for a fraction of a second. It takes a little practice to get the timing right, but it will become second nature. You will be rewarded by pretty much the smoothest, quickest gear-change you've ever come across on a bike.
As an aside, I mentioned that I only use my forefinger to change gear. To expand a bit on that, different riders have different preferences. A fairly common one is to use the finger to change up and the foot lever to change down. On my first YCC-S bike, I chose to deliberately not use the foot lever so that I had a reminder that, if I rode a conventional bike where I had to use the foot lever, I needed to use the clutch! I first started using forefinger to change up and thumb to change down. But I found this clumsy, and frequently sounded the horn instead of changing down. Finally I ended up using my forefinger either pulling or pushing the finger part of the switch, makes for very rapid up and down changes. I've always preferred to stick with the finger, leaving the foot completely free for putting down when coming to rest. The finger is also better at timing than the foot.
Not directly relevant, but just to add that having had two Gen 2 YCC-S bikes, I am now fortunate enough to have a Gen 3, unavailable as a YCC-S in America. It takes advantage of its throttle-by-wire and you don't need to adjust the throttle manually, it does this for you, optimising throttle and clutch during any normal change.
