I'm no expert and I haven't done enough cars to ever call myself a pro. I'll lend a little advice from a fellow home garager...
First thing (And most obvious) is to clean the heck out of your surface before you spray and every time after your surface dries with a tack rag. Do it on every layer. Don't get lazy. Wipe the car down with a tac rag. EVERY DRY LAYER. Your surface can never be too clean. You may be getting some dust/dirt falling from your cealing or somewhere in the garage. Clean the whole garage. To the point of insanity. I paint in my home garage and you'd be surprised how much dust just sits WAITING for you to paint. You may want to consider actually covering the cealing and walls of your garage with plastic sheets just to catch the dust. I know this is kinda basic, but so many people underestimate the power of hidden dust.
As stated above, strain your clear. NEVER leave the can open longer than you need to. Dust, much like a virus, sits around wating to hop in your clear and make your life miserable. Make sure your clear is clean. Same for your gun (Which may be the villan here). Make sure it's clean. Use a different gun for paint/primer-sealer/clear. This looks very much like theres some primer in your clear TO ME, but it could be dust or old clear. Make sure your clear isn't expired or close to being expired.
The stuff mentioned above you probably already did and checked. The gun is new, so as long as you're cleaning really good between surface changes then that eliminates the gun. If you used chemical stripper then yes, you do have to nutralize it, but if you're washing the car good that should help. I'm also assuming you did nothing like constantly touch the surface with bare hands, but that wouldn't cause trash.
Hell, strip back down to the primer layer. Even things out. Prime, seal and paint again. If it happens again, go buy some more clear, another generic gun JUST for clear and try again. I know this probably doesn't help but that's what I would do.