What are these dark spots in donor area after FUE?

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