The below image gives a representation of the hair follicle and blood vessels.
When a particular area is heavily extracted (over extracted) this can cause excessive trauma to the area in general including damaging blood vessels below the scalp surface which can negatively impact their efficiency and how they are able to provide for nearby follicles. This can influence hair groupings and/or the diameter and strength of the hair structure, adding to the visual effect of an over-harvested donor area.
The skin dermis contains blood vessels, nerves and other structures. Any cutting or damage to the dermis can affect blood supply and nerves and even more so when considering the subsequent healing process of scarring after any damage to the tissue. Scar tissue will have an impact on blood supply.
Another factor is considering the size and angle of the punch. The larger the punch, the more tissue is effected, and if less perpendicular (more angled), this will also increase the surface area of tissue.