I have fought the same issue. For me it all had to do with the right wrist. It is hard to explain, but if I kept strong hand wrist more straight, the problem goes away. I am still trying to get it down subconscious. I do disagree with the person above. It is a terrible problem to have (almost every penalty i get is from pulling the second shot low) because most NS and hard cover is beneath the target so unless you were shooting doubles beyond 15 yards, it is worth taking the time to fix. My theory is that in my attempt to reduce right hand tension, I was moving my right wrist tension (and position) with my trigger finger. When i release the trigger, i unlock the wrist and the gun goes up and when I start to pull the trigger again I relook the wrist and gun goes down. My reasoning is I noticed that when I pull the second shot low, the gun recoils more so it’s not me actually trying to push the gun down.
i have experienced this on multiple platforms and different types of ammo