Many times it's not what we did wrong....it's what we didn't do right.
It may very well have nothing to do with how or what you sealed with. It can be a little tricky but in certain instances I have shot clear directly on to wood with no problems.
In order to figure out what has caused your "problem" you'll have to start at the very beginning of your system.
source of air.....
line pressure...
line filters....
line desiccant....
gun used.....
material used....
humidity at the time of spraying....
This is just a short list of items that may need to be addressed in an attempt to lay out the perfect clear coat on a project.
Anyone of these or a number of others could be the source of contaminants and reason for what you are describing.
Only then can you start looking at the project and how or why you used certain sealing methods in your attempt to lay down a flat, water clear jacket of protection that will last for many years to come.
Or, it may very well just be the operator has messed up and not sprayed according to spec.....example, laid the material on too thick or too fast between coatings.
The art of spraying a quality clear coat is a science within itself. Then....just when you think you have it all figured out, it'll smack up you upside the your noggin and having you asking yourself. WTF happened this time?