If you're consistently low, without even realizing it, you might be looking for your hits on the target instead of performing a proper follow through. What that means is that once the shot breaks, you're unwittingly looking over the sights at the target and in so doing, the muzzle is being lowered ever so slightly to provide your eyes with a clear line of sight to the target.

This is one of the more subtle and nuanced errors that shooters commit. Because humans are visually oriented animals, we're very intent on visual feedback in most everything we do.

The mechanics of what may be happening is that BEFORE the bullet exits the muzzle you are depressing the muzzle thus canceling the sight alignment you had a microsecond AFTER you pressed the trigger.

It seems ludicrous that a shooter can depress the muzzle to look at their hits on target before a 9mm with a muzzle velocity in the neighborhood of 1100fps exits the barrel but it happens.

I agree with others that dry firing will help with flinching and as you already recognize you have that particular problem. However, proper follow through will eliminate the "looking over the sights at the target for my hits" problem.

Proper follow through is that once the shot breaks, IGNORE the urge to look at the target. Focus on reacquiring the front sight, reset the trigger, and reacquire a sight picture in preparation for the need of a possible follow up shot.

HTH