With the limited information and without seeing the shop it is darn hard to say anything. Barry's info on solvent pop would cover that subject.
Let's go down with the most common.
1. Solvent pop (that is why I mentioned it) it can happen pretty soon. How soon did this occur? Hard to say, one mans "as soon as I applied the clear" is another mans ten or fifteen minutes later. It still could be solvent pop. Look close to see if there is a "volcano" look to the craters formed by the solvents rushing out of the "film" on the top of the clear.
2. Contaimination, DIRT, yep, "bondo" dust can look exactly the same as discribed. As soon as a nice coat is applied the top starts to "film" from the solvents evaporating. The tiny dust particle (too small to see without looking REAL close) falls on the "film" and sets there a while before it falls thru, wham, a "fish eye". These can be seen if you look real close. The spec is sometimes seen at the bottom of the crater. Plus, the top of the crater doesn't have the "volcano" look.
Any other contaiminant such as a wax or something, very unlikely. These flaws appear only on the top surface or mostly on the top surface.
If it was something in the line, water or whatever, it would be all over. This is one of the first misconceptions with "contaiminants". How in the heck could it be only in one area if it was "in the gun"?
3. Towels, again, nearly impossible being it is only in one place.
"When you hear hoof noises think Horse not Zebra".
Start at the most common (likely) and work down.