I'm finding exactly the same message, despite at least 60%charge on the phone.
Not sure if it's a coincidence, but the first time I noticed this message was just after my daughter used the car and linked her phone to the car.
Be interesting to see if others have similar experiences.

 

I contacted Skoda UK, They told me to try a few things, a hard reset on the info system has seemed to have got rid of the warning...for now?
I held down the power button on the info system while car was running for 20 secs, it rebooted and now the charging message has gone.

 

I find that the 22 plate Kodiaq onwards, until the Mk.2 had horrendous problems with the infotainment system. I had a U2 plate Sportline and the infotainment system constantly crashed and the updates never seemed to resolve their problem problems. There were many occasions when the streering whell controls failed.

the wireless charging wasn’t the best either, never managed to get a consistent charge, and in was slow and cooked the phone slowly.