This problem has nothing to do with the clear! The dead giveaway?
How long it took to occur.
Solvent was comeing up from deep down.
A couple of things will cause this.
Very common on Black, Dark blues and some reds as they are slower drying colors and piling on, to short of flash between coats, using to big tip for base. using to fast reducer for the outside temp in base, ANYTHING to trap solvent in the base, in other words.
Second cause but more rare is a lacquer sealer being used or a sealers with trapped solvents.