It's highly unlikely the peel comes from the basecoat layer as this layer is thinest of all but phosphate. More than likely clearcoat and there are many reasons as to why this happens.
I've read many posts regading measuring the film thickness using an elcometer or similar gauge. While I believe this to be a good tool it is also important to remember this reflects the total of all layerings (phosphate, ecoat, primer, basecoat and clearcoat). My experience with automotive...