Here are three different sight pictures.
The first is common, often referred to as a six o’clock or lollipop hold. It is used primarily for target shooting, with a specific size black target at a specific range. It is actually a poor choice, as bullseyes can be of different sizes, at different distances, and the actual alignment can look good but still be imprecise (especially on an all black target without the “crosshairs”) because it is based on being somewhere close to the bottom middle of the edge of a circle.
Number two tends to give more precision because it overcomes most of the weaknesses mentioned above.
Unfortunately, some defensive guns use the third alignment, especially those with three dot alignment system. In truth, the front dot is not supposed to indicate the Point of Impact (PoI). The three dots are just supposed to be sight alignment (SA) aids leading to sight picture #2. But some guns seem to shoot at close ranges using #3. The front sight covers the point of impact because some experts claim you concentrate on the front sight and put it right at the point you want the bullet to go. This works well at close targets, but it obscures the target at longer ranges and makes accurate shots less likely.
Mass manufactured guns usually use #2. However, they are mass manufactured so slight variations in dimensions, lockup, and ammo used can add up to some real PoI variations. The actual distance to target for both Point of AIM (PoA) and PoI can also vary. While many believe 20 yards is a common distance for concurrence, it is often closer.
For you, try some different ammo, such as heavier bullets.
Try a different SA.
Try your SA at 7, 10, 15 then 20 yards.
If all of these suggestions fail, your best option is to use the sight height calculator at Dawson Precision and order a new taller rear sight from the manufacturer of your choice.