I've had exactly the same issue with my Milano FN2 since the first week. The bonnet and front wings now look like someone has thrown a bottle of tippex over them.
Anyway after nearly 12 months of trying to get Honda to respond to me I finally blew my top and emailed the head of Honda UK customer relations (after not getting promised callbacks and being ignored for months). Within about 30 minutes I had someone call me and arrange an independent paint inspection and I also had a call from the dealer that same day about some other issues I'd had.
The paint inspection was carried out (I'm not convinced it was that independent as
HUK arranged it), but the report came back that the stone chips were a road hazzard and not Honda's problem.
HUK have now offered to pay for 50% of a bonnet and front wing respray as a goodwill gesture.
Be tenacious, you might eventually get somewhere with them if you keep trying....The paint is clearly carp on the Civics, My other half bought a Megane at the same time, same mileage as my car now and not a single chip on it, says it all really.