It is possible that it is what I call the 3D effect (one reason why I never applied clear before doing touch-ups)...If you repainted after coats of clear the paint is on a different level than the original and will have a kind of 3D look to it...so to speak...
As others have said if the inserts were lower to begin with clear needs to be dripped around the edges then after it is dry sanded down to make it level then apply coats to the entire field or the low spots will never catch up with the rest.

Phoebe