What are these dark spots in donor area after FUE?

There is no way to say what you are seeing from a sentence on the Internet.   It may be best for you to contact your doctor for a follow up exam or email your doctor some photos.

hailmary,Most likely you are seeing small crusts in the area, since the punch sites are left to heal by secondary intention.Sincerely,Bernardino A. Arocha, MD

With such little information there's no way to make an accurate guess. 'Dark spots' could mean so many different things. You should ask your doctor about it, but they're likely just scabs that haven't been washed off yet.

Without a photo I can only assume you are referring to the crusts/scabs that are normally seen the first few days after the FUE.  Your hair transplant surgeon/staff should have gone over with you the post op care after your procedure.   Contact your hair transplant physician to ensure that you are undertaking the necessary steps to obtain the best outcome.

I suspect that what you are seeing is crusts from the actual graft placement that was not washed off in your normal post operative care.  See photos below