We are facing the same question - have recorded our displeasure in writing and will also include it in the protocol during the final inspection. On the outside, we were able to conceal the error, inside it is not as visible as with you. But the countertop in a separate part of the kitchen will now be almost 2 cm higher than planned. I don't think that's great, but it's not overly dramatic either.
Could it be visually concealed for you by adjusting the height of the inner window sills slightly?