This isn't particularly our area of expertise, but I'd recommend trying to play music from your phone via Bluetooth. That way you can ascertain whether it's an issue with the phone, the USB port or the cable itself. If you can listen to music via Bluetooth without the feedback/noise you're experiencing via the USB port — I'd recommend buying a higher quality charger and seeing how you get on.

If that doesn't work, I'd suggest getting Skoda to take a look at the car. This shouldn't be an issue on a new car and should hopefully be resolved under warranty if it's an issue with the car itself.

Unfortunately, having looked at a few Apple forums about similar issues from various readers —Apple's firmware does seem to display these sorts of issues sometimes, especially on older iPhones. This means it could be an issue with the software on the 5 SE, despite you having updated it to the latest settings. If it turns out that it's likely to be a problem with the phone (through a process of elimination) and you're fine with the phone and not planning to change — it may just be something to live with. However, if you are planning to upgrade, you may find that a newer phone doesn't have these issues. I only say so because Apple stops issuing software updates for older iPhones after they've been out of circulation for a few years. I believe your 5 SE launched in 2016, however, due to being an SE, I don't think it can have some of the most comprehensive updates (like iOS 13).

This is purely anecdotal, but we do get more reports of issues about phone connectivity in cars from readers with older smartphones.