This is very frustrating and I have had this a couple of times, though usually repairing old parts. The essence is the top coat volatiles, i.e. thinner, carrier solvents etc are leaching down into the substrate and reacting with it. It can be non compatible chemistry or simply cellulose getting under a drying topcoat and softening the primer which then contracts at a different rate, causing the crinkling.
As others have said, it can also be unclean substrate causing a poor adhesion of primer, which is why surface prep prior to priming is so essential. The quickest solution is to DA back to bare aluminium and re prime and re finish.
If you end up repairing old parts, thoroughly clean and de grease with a good non salt bearing detergent like Dawn, then when dry you can apply a coat of Bar Coat or similar which is an alcohol based lacquer. It doesn't react to the cellulose substrate and allows different chemistry to be applied above. It is particularly good on composite parts.
The other time it can appear is if you have used fade out thinner to combat runs or blebs. The Xylene in it is very penetrative !
Very annoying but not the end of the world.