That sure as heck can cause problems. An expericanced painter can have a heck of a time, don't feel bad.
Listen, this is the lesson of the day
"Solvent is the cause of 90% of failures". The solvent doing "something"; to fast, to slow, to slow a gun movement, poor atomization at the gun, too large a tip, to low air pressure, SOMETHING that is changing the way the solvent flashes, that is the root of 90% of painting problems.
In your case you were using WAY too slow of reducer. I was thinking S-W not M-S and I wasn't thinking Cross/FIRE at all. Cross/FIRE is an "OK" product. You have to remember it is a "Value line" product. Like PPG's OMNI, DuPont's NASON, they are "OK" products and will save you some money (sometimes) but they are not top of the line and will not by the odds give you as nice a job with the least effort.
That aside, that reducer was WAY too slow. CR236 is the "extreme desert" condition reducer recommended for 100 degrees, that one isn't even at the 110 you were at! Again, solvent (anything used in any paint that lowers viscosity it would be alcohol, water, lacquer thinner, enamel reducer, anything that is in the product or added to the product to lower viscosity) is the cause of your problems.
You likely had to "bomb" the paint on, the solvent flashed off the just the surface of the paint film, trapping solvent inside. That solvent pushed it's way up thru in between the color and clear creating poor adhesion. That is likely what happen with the info you have told me. The paint not skicking to the primer is unclear. I am thinking you used a wax and grease remover prior to paint that didn't totally flash off or something along those lines. However, with a really fast flashing solvent in the base, that could have caused the poor adhesion as well.
You do NOT need to bomb on the clear to make it "lay smooth". A fine atomization at the gun and a thin layer of clear will do it. The first coat should look like the last, one even good overlap (50-75%) with NO "holidays", I mean it, it should look like you are done. That is how BOTH coats should look.
You CAN apply the clear like this if the gun is properly set up, you have enough air VOLUME, and you apply it as described. It will go on without a run, and be as smooth as you dare to get it.
Does this make any sense?