Bald Spot generated after 3 weeks post hair transplant. (photo)

You did not supply any pre-operative photos so it's impossible to determine what is going on here.  Grafted hair is supposed to fall out naturally after 2-3 weeks.  If the hair does not fall out, pimples will often form as the body uses pimple to help eliminate transplanted and non-growing hair follicles.  It is also possible to get shock loss in areas where follicles are transplanted.  This could also be what is going on with you.  The rest of the area does not looked inflamed based on the photos you submitted so I suspect you do not have an infection.  Go back to your physician and have him evaluate your condition.  I suspect nothing serious is going on, but get his opinion.  He knows best because he had the value of seeing your situation prior to surgery and how you currently appear.  

If you have an infection follow your doctor's recommendation and treatment plan.  Only time will tell if your hairs will grow back.

It is not uncommon to see uncovered area at this point after your procedure.Many of the transplanted grafts may have fallen out and there may have been some shedding of native hair.With time (6-12 months) this should all grow in.Typically grafts will grow back in areas of folliculitis,however if the infection is severe enough there may be some loss.Again,time will tell.

Yes, because of the folliculitis (or any infection) is it not surprising that you have a small bald spot at the location where it occurred. Your doctor is right- generally hair will grow back in that area but there is a chance it won't. There's nothing you can really do about it now except wait and hope for the best. Having a small touch up transplant surgery shouldn't be a problem if the hair ends up not coming back.

Go back to see your doctor to make sure that it is nothing more than reactive localized hair loss and not some other type of problem