The Super Knob is surrounded by red LEDs, perhaps you are referring to the LED lights that show up from under the Knob cap. You are making an assumption about the shading and color schemes. They vary greatly. Each glow pattern has an identifying number... and a different pattern when moved.
From the main HOME screen touch “Motion Control” > “Super Knob” > find “LED Pattern”

I am sorry, I mean the LEDs under the knob, not around the knob. And it hasn’t got anything to do with any kind of setting of Motion Control or the LED pattern. It occurs in any constellation or setting. See the photo ...

Here is a photo ...

Have it checked with a service center - certainly if within warranty.

If the problem is LED component failure - then the fix should be very minimal in terms of hours and component cost. It would be on the least expensive end of the repair spectrum (not necessarily "inexpensive" - just the lowest end of that spectrum). That is if they just replace the LEDs individually. Today, repair means swapping out boards. The PNL board would need to be replaced and this is relatively more expensive then fixing the PNL board. I don't have pricing on the PNL board but these seem to generally run in the $200-$300 range for the board itself. Which is lots more, in terms of parts, then $0.60 per failed part for the RGB LEDs (plus shipping). This may not be the problem (as the board layout doesn't seem to position the LED exactly where the color is missing in your picture) - but point being that a service center that's comfortable with component swaps will land you lower on the cost spectrum if you're out of warranty. If you're in warranty - then board swapping would be best as it's better to have factory placed/soldered components in terms of reliability than reworking a board. That said - I'd be more than fine with reworking my own board as I know I could rework just fine. So the sky is not falling certainly if a capable technician is doing rework.

Ultimately, if you're under warranty - it doesn't matter how they fix it. I'm only supplying some detail in order to convey some sense of the relative costs for the two approaches. Which may help guide your decision if purchasing out-of-warranty repair services. If money is no object - then deferring to the wisdom of the repair center is best. If you need tighter control over the expenses - then you may be able to find there's less expensive routes particularly if you initially get quoted an invoice based on board swap.

Thanks for the advice!
Tomorrow I will bring it to a service partner of Yamaha, since today in the morning the screen startet flickering in addition to the problem with the SuperknobLED.
Holy sh***! Hope they can fix it!

In my experience flickering screens on Yamaha equipment has been a function of the storage and operating humidity of the device (more humid, more issues). Interconnect is usually the issue - and certainly high stress ("shock and vibration" ) of the unit can affect internal cable seating. It's more rare for a "shock and vibe" event to happen that would impact interconnect. It has to be fairly severe for that.

None of the above speculation really matters as the service center will do whatever is necessary. Generally reseat the cables then swap out parts if that doesn't fix it. So your range of costs there can be just the bench fee (essentially no parts cost and hardly any time on the bench - meaning close to 0 hour) or fairly expensive if they feel the touchscreen needs to be swapped out or if the interfacing PCB needs to be swapped out. The touchscreen itself is an assembly with cables inside the assembly. These tend to be very delicate and not generally something a service center will service (inside the assembly) - which would mean a touchscreen swap. I haven't seen what your warranty status is - but you're covered no matter what if there's a defect and the touchscreen needs replacement.

By the way - flickering touchscreen and an LED that doesn't turn on can also be power related. The LEDs are powered off 5V. If 5V drops below 3.3V then the LEDs would be very close to the minimum forward voltage in order for the LED to illuminate. And this may also cause touchscreen flicker if the same voltage rail is employed there (I haven't double-checked the schematics). Now if 5V drops below 3.3V - that's very drastic and likely nothing would work. USB shouldn't work lots of things shouldn't work and possibly the unit wouldn't even power on with a rail so poorly out of regulation. But just one not-so-probable theory that the flickering and superknob LED failure could be related.

Again, none of this really matters as the service center will do what it does to diagnose.