It is only one of two things and has nothing to do with expanding at different rates.
If you can wet-sand and buff out the scratch, then is is bad buffing, I won't go there, because what you are explaining is a SOLVENT trapage problem in the first coat of base.
First of all the car needs sun for a full day:
If you cannot buff out the scratches, then what it is you trapped solvents in the first coat of base, by either using too fast a reducer for the temp at hand or you just plain put the second coat of base on too fast, the solvent is setting there trapped and as you heat it, it expands and tries to escape and because paint is not airtight it does move and then you are left with a scratch showing.
It needs sun ASAP as the longer the solvent sets there it can swell a 600 grit scratch into looking like you painted over a 80 grit scratch and you further increase the chance of the solvent breaking adhesion between the clear and base.