When I see "a light coat of clear" that is all I need to see. Wrinkling is caused by solvents getting thru, or under an edge of a previous substrate. It could be years old as in a 1k enamel sprayed over a poorly sanded original paint. You sand a chip out and now the next paint or primer you spray the solvent in it gets under the edge of that old 1K enamel and lifts it up wrinkling it. It happens in that case because the enamel isn't sticking to the original paint good because of the poor sanding, and it's a 1k and the solvent soaks into it easy on the edge.
The exact same thing happens when you spray a "light coat" of clear, it isn't a barrier, the solvent from the next product soaks thru it and lifts it up wrinkling it.
There are other things that could be at play here such as recoat windows, there is a time with some products that you can respray it, be it two hours, or after 24 when it is more fully flashed and or cured.
It's kind of a partially cured paint or clear is like a too thin sheet of protection. The solvent from the next product soaks thru that thin top layer that has dried and gets under it, much like the old 1K enamel example.
But I am thinking if I read your post properly it sounds like the thin coat of clear is the problem.