Is tiny black stubble a bad sign after FUE? I'm 3 weeks post op. (photo)

Hi and thank you for the photo's!
It appears things are progressing nicely.
It's nothing unusual to see what you are seeing especially if your hair was in the growth phase when it was relocated.
Things will slowly improve month by month all the way to 12 plus months.
Make sure you go back for follow up visits with your doc during the first 12 months so they can track your progress etc....

It is not very clear what the black dots may be but it can be tiny hair follicles starting to grow in.

tiny black dots/stubble are indicative of open follicles that are alive and healthy.  It means that things are progressing along as they should.  Congratulations on your procedure, and you will certainly enjoy the journey over the next few months as the little follicles start to grow! 

Your hair transplant recipient area looks fine to me but I can't see the black dots you are talking about