Potential issue 1: Paint+Primer combo. I've never used one but I've heard they're not as good as straight primer then straight paint.
Potential issue 2: Gloss finish on the Paint+Primer combo. Once a gloss finish dries it doesn't take additional coats as well as flat. I no longer use gloss paint. I use all flat to maintain toothiness on each coat. I then nuke it with clearcoat at the end for shine and durability.
Potential issue 3: To me those patches suggest contamination from skin oils or the environment.
Was the glitter can THOROUGHLY shaken and mixed?
My last rocket above followed this formula (All Rustoleum products):
Day 1: 3 coats of gray primer (next day sanded to remove imperfections, wiped clean)
Day 2: 3 coats of flat color (next day lightly sanded to remove imperfections, wiped clean)
Day 3: 1 new coat of flat color, then 1 coat of glitter (additional glitteriness could be achieved with additional coats, that wasn't my goal on this job).
Day 4: At least 10 coats of clearcoat
This was done in a paint room at work at about 65 degrees, <30% humidity, with four high-intensity lamps overhead.
I also put it on a horizontal jig with a rod through the motor mount where I could turn it 120 degrees at a time by touching the masked exposed motor tube. At no point in the painting process did any surface of the rocket touch anything.
Each day I applied coats 10-20 minutes apart. First coats were light to establish a tacky base for the next coat. Second coat filled in gaps and built on the tacky surface. Third coat was the heavier finish coat where complete coverage was achieved, ideally with no runs.
I personally don't go the extra mile and wet-sand with ultra-fine sandpaper in order to achieve a mirror finish. If it's relatively attractive and smooth I'm fine with it. I figure the more time I put into a flawless finish, the more likely I am to CATO the thing on its first launch.
Disclaimer: I don't claim to be a paint expert, I just know what has worked for me.
If I were in your shoes with the Scorpion, I would lightly sand it with 400 grit, wipe it clean, lay down a couple new coats of that gloss primer/paint, but then apply the glitter within a half hour while the gloss is still tacky. FWIW the glitter leaves a sandpaper-like finish, so you probably want to clear coat it at least a few times to seal in the glitter and improve the smoothness.