Some sights, particularly for self defense, are registered so that you COVER the desired point of Impact with the dot of the front sight. A large front dot with a simple rear is typical of this kind of sight. Precision is not as important with these sights as quick acquisition and alignment for self defense purposes.

A more precise alignment comes with target registered sights where the point of impact is ABOVE the front sight. If you use a target hold with defensive sights you will get the results you are experiencing.