I have had the same problem with my Octavia automatic-  low mileage just out of warranty.

 

Today the dealer has diagnosed the fault and want a mere £909.86 to fix it. They are asking Skoda for contribution for this.

 

Apparently they have to dismantle and replace the entire gear selector mechanism.

 

A bit steep for something that is probably  a 50p microswitch.

 

This does not affect the driving, but it is a definite safety hazard because of the "alert" beep.

 

Awaiting reply from dealer.........

Mine is also doing it intermittently - 1 month out of warranty, think I will leave it....

Common problem if you search the forum.

 

By the time I sold mine it was on it's third gear lever assembly.