I don't know what is causing the problem, but I have a suggestion to help you solve the problem.
First, as Weather Vane says, do not attempt to repair or alter this vehicle or take it for repair to anyone other than a Skoda dealer. The car is new, and any defects should be fixed at no charge under warranty by the dealer. You can void your warranty if you attempt a repair any other way.
Record video with sound to document exactly what is happening. Set up your phone or a GoPro or any other video recording device on the passenger seat or affixed to some other place in the car. The video should clearly see your feet and the gear shift lever. Leave this set up recording for all of your driving until the bad sound happens at least one time. No music! You want to hear the bad sound on video.
If you are doing something wrong to cause the noise, it will be revealed in the video. But if you are doing everything right and the car is malfunctioning, you will have proof. Video doesn't lie!
For example, if you shift into first gear but (without realizing it) you pull back on the shift lever slightly before you release the clutch, you will see this in the video.
Another example, if the shift lever goes all the way to the right position for first gear and you take your hand off the shift lever, but the lever pops out of gear when you release the clutch, you will see this too.
Also, once you have video proof that your new car is malfunctioning, it gives Skoda a very strong incentive to fix your car. They certainly don't want to see a video like that posted on social media.