Why do some patients have defects on the skull around the areas where the patches of Alopecia Areata are located?

It is not clear what you are referring to.  Some people may be born with "defects" or irregularities on the scalp.If you have alopecia areata and have had STEROID INJECTIONS, that can also cause depressions (inward dents).  It is one of the side effects of using steroid injections.

Some people have indentations in the skull and with hair loss, it can appear to have divots that fill in with hair regrowth. I suggest seeing a hair loss expert to evaluate and go over your condition and provide you information about your best treatment options. There are great non-invasive options like PRP/progesterone and/or hair transplantation. See an expert. Best, Dr. Emer

If
there is an area of soft tissue depression of the scalp associated with a patch
of alopecia areata it may be related to steroid injections.  Steroid may dissolve the subcutaneous fat if
it is given too deep or two concentrated.  This is something that may or may not be
reversible. You need to be examined by a hair specialist for that.

These skin depressions usually come from steroid injections.  The phenomenon you are describing is called "atrophy". The indentations are temporary provided the clinician does not keep injecting into the area. Otherwise in alopecia areata there should not be depressions if the patient has not received steroid injections.

When hair is lost, the scalp in the area of lost hair loses its fat and looks as if it is depressed into the skull. When hair grows back, these divots disappear.